You should backup everything(save an image of whole drive) before continuing.
Another thing is if you have your system running you can change physical position of OS on drive.

Thank you EDDY1,
Can you recommend me some tutorial on back out the whole image or the drive and methods moving the position of my OS on drive?

best,

Do you have another drive?
If so using clonezilla, you can save images of whole drive or individual partitions.

This 1 is for whole drive.
http://linuxgravity.com/creating-and...with-clonzilla.
There's an option to save images of each individual partition that's your best option as you'll be able to selectwhich partition you want to restore.
Btw syg00 has much more experience, so you may want to request his help as I'm a newbie.

Clonezilla is a good suggestion.

For moving the partitions, use gparted from a liveCD - note you *cannot* do this safely from the running system.

Thanks to EDDY1, I will try this one. But currently I only have 320g usb driver while my main hard driver is 500g. I will look into it.
Also thanks to syg00, I will follow your advice and try to get my OS moved to right place.

Cloning is good idea, safe and simple if you have enough free space.
Anyway you won't loose any data by deleting swap partition, which is /dev/sda4 unless you don't understand partitioning. Deleting it and creating new logical swap partition will asign it /dev/sda5 or above.
Correct it in ubuntu's /etc/fstab using liveCD.
You can assign as many new logical partition as needed.
Remember one disk support maximum 4 primary partition, reason for missing disk space.
Backup of /home directory should suffice if you haven't stored any data elsewhere.
If you have made configuration changes then backup /etc directory.
Backup /var/www and your database if you had your webserver setup.
Backup of Ubuntu system is unnecessary if you have it's DVD and not installed any custom packages or drivers.

I parted my disk again and got the missing part back.
Here is what I did:
Boot the system with ubuntu live usb.
Run parted on sda: part /dev/sda
Change unit to sector: unit -s
Remove the sda3: rm 3
Create the extended partition, using all the unused part of the drive except a 2g partition for backup.
Recreate a logical partition sda5 on exactly the same place of original ubuntu os root i.e. original sda3.
Move the win7 partition (original sda2) to the right and resize it a little bit.
Fix the grub in MBR with grub-install --root-directory
Now my system is ok to use without losing any data.

While I have two problems right now:
1, The win7 can not boot. I searched a solution said I should use a win7 installation disk to repair the win7 partition. I am working on it.
2, There is still "Partition 1 does not end on cylinder boundary." This is very wired since I already move my partition to the right and leave about 8m space between these two partitions.

/dev/sda1 2048 206847 102400 7 HPFS/NTFS
Partition 1 does not end on cylinder boundary.
/dev/sda2 224910 81947564 40861327+ 7 HPFS/NTFS

Can anyone tell me how to fix this cylinder boundary problem?

Disk /dev/sda: 500.1 GB, 500107862016 bytes
255 heads, 63 sectors/track, 60801 cylinders, total 976773168 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x3ef75c5c

Device Boot Start End Blocks Id System
/dev/sda1 2048 206847 102400 7 HPFS/NTFS
Partition 1 does not end on cylinder boundary.
/dev/sda2 224910 81947564 40861327+ 7 HPFS/NTFS
/dev/sda3 81947565 972671489 445361962+ 5 Extended
/dev/sda4 972671490 976768064 2048287+ 1b Hidden W95 FAT32
/dev/sda5 * 482035712 968364031 243164160 83 Linux
/dev/sda6 968366133 972671489 2152678+ 82 Linux swap / Solaris
/dev/sda7 81947691 278792009 98422159+ b W95 FAT32
/dev/sda8 278792073 482030324 101619126 83 Linux

sudo os-prober
sudo update-grub

thank EDDY1,
But my problem is not in the grub menu. I did have the win7 in my grub menu. But when I choose the windows7, it turns out "there is some change in hardware, please insert your installation CD and choose repair."
I am looking for win7 boot CD now.
Any idea about the "Partition 1 does not end on cylinder boundary" problem?

If you can't find disk you can download recovery coinsole
http://www.proposedsolution.com/solu...overy-console/