I have MSSQL 2017 installed on Centos 7 server. The stored procedures run very slowly. Comparing to the same hardware settings Windows 2012R2 sever, Centos SQL query speed is only one percent. Could anybody please give me a hand to resolve this issue? Thanks.

We'd be happy to try, but you haven't given us ANY details to work with. Server statistics? DB Size? The stored procedure in question? Times? Anything???

Since you're using MSSQL...have you contacted Microsoft for assistance? It would not be very surprising if a Microsoft product was engineered to run better on Windows than Linux to start with.

The server is a VM of Centos 7(3.10.0-514.26.2.el7.x86_64) with 50GB RAM and 500GB HD, and DB is of size 6.7GB. This DB is originally developed on MSSQL 2012 on Windows 2012R2, and all SPs are running smoothly on Windows. As business progressing, there is need for a new SQL server to share the workload. Monitoring the stored procedure with SQL Server profiler, the SP:StmtCompleted event, with duration filter 100ms, shows more events counts Linux/Windows 14/6, longer duration 2600/300, longer CPU time 32000/200.

The server is a VM of Centos 7(3.10.0-514.26.2.el7.x86_64) with 50GB RAM and 500GB HD, and DB is of size 6.7GB. This DB is originally developed on MSSQL 2012 on Windows 2012R2, and all SPs are running smoothly on Windows. As business progressing, there is need for a new SQL server to share the workload. Monitoring the stored procedure with SQL Server profiler, the SP:StmtCompleted event, with duration filter 100ms, shows more events counts Linux/Windows 14/6, longer duration 2600/300, longer CPU time 32000/200.

Ok, so is the Windows server also running in a VM, or on a physical server? And what kind of VM? How is the storage attached? And 50GB of RAM...with 500GB hard drive? 6.7GB database size? Is that all on one spindle?

Still lots of variables unknown here. If the MS server has the OS one one drive and the DB on another, it's going to be faster than a single-spindle system. Virtual Box vs VMWare ESXi is different. Again, using a Microsoft product on Linux will probably not get you the best results, but it may also be in how you deployed it too. Have you contacted Microsoft for help with this? They may be able to assist in tweaking things.

Both servers are VM on Hyper-V. Linux is on one spindle, but Windows is not. I wonder if there is a way to configure Linux drive for MSSQL as Windows.

(bold added for emphasis)....ANY database running on multiple spindles will be faster than single, regardless of OS. And you configure the Linux server same as you would for Windows (generally speaking). Format the disk, mount it, and put your application/database on it. Most of the entire Internet, all of the worlds fastest supercomputers and largest databases are all running either Linux or Unix.