I connected two 3.5 HDDs via SATA cables.
I also connected my external seagate desktop drive 6tb 3.5 internal connected via usb.

I notice that when I shutdown my Linux... My HDDs power down, but my seagate is still spinning.
Anyone know why?

------update reply----
Yes, the seagate comes with a separate power cable.
This setup was meant for remote file server usage. If I unmount the internal HDDs then they become quiet and seem to stop spinning.
If I unmount the external usb seagate, it still spins albiet slowly.
I was thinking maybe it's motherboard config..
I also own another older seagate but on my windows pc and am sure it auto stop spinning when no usage after long period.

sometimes those usb ports remain powered (even when you shut down your computer).

Usually a 3.5" installed in an external case requires 12 VDC provided by a separate power supply. Mine which are really old have a power switch. If yours doesn't have a power switch the 12VDC might be turned on by the presence of USB power. As stated if the USB port remains powered it would keep the drive spinning but you can test it by just pulling the USB cable after the computer is powered off. If the drive does not stop spinning and there isn't a separate power switch then you will need to unplug the power supply when the drive is not in use.

Yes, the seagate comes with a separate power cable.
This setup was meant for remote file server usage. If I unmount the internal HDDs then they become quiet and seem to stop spinning.
If I unmount the external usb seagate, it still spins albiet slowly.
I was thinking maybe it's motherboard config..
I also own another older seagate but on my windows pc and am sure it auto stop spinning when no usage after long period.

Many USB to SATA bridges don't support SMART commands and won't allow drive to suspend. Run smartctl to check - if it doesn't detect this drive as SMART-capable, your disk cannot do it, and if it does you can set it up any way you like.