In contrast to most other software, OpenMPT actually cares to really save your data to persistent storage. By default, Windows (or other operating systems) do not write saved data immediately to disk, but instead keeps it in its internal cache for some time in order to improve performance. OpenMPT however explicitly flushes the saved file's data cache to disk before continuing.

You can disable cache flushing in OpenMPT by setting the hidden setting [Misc]FlushFileBuffersOnSave=false (see https://wiki.openmpt.org/Manual:_Hidden_Settings#.5BMisc.5D) in order to improve performance.
However, PLEASE NOTE that this will cause data loss if your system crashes some time AFTER saving (I'm not sure about the current write-back policies in Windows, but I would guess something in the ballpark of 30 seconds).

VST Plugins could also additionally contribute to longer save times.

What kind of disk/storage are you using?

Also, which version of OpenMPT did you use previously?

Cache flushing was added in 1.28.

Also, please provide the song that is taking 12 seconds to save, because without knowing how many samples or VST plugins you use, it could be entirely expected.

PS: Feel free to switch to MilkyTracker. I see you edited the bug description since you submitted it so maybe you regret your childish comment already, but empty threats like "I WILL SWITCH TO SOFTWARE X IF YOU DON'T DO Y!!!" don't help anyone and will in fact make it less likely that I will be willing to help solving your problem. Use MilkyTracker as much as you want, I don't care. I even contribute to its code occasionally.

Ehh, personally, I prefer... both!

I disabled cache flushing, but it still takes a little long; 10 seconds at best. Any other ways?

Without providing the requested information it's hard to tell what the issue is:

1) the actual module you are trying to save and
2) what kind of storage media (hard disk, SSD, USB 2.0 flash drive, etc.) you are trying to save it to

You can mark a comment as private if you cannot share the module publicly.

Update: The module had long save times because of some large "reference" samples, which I removed.

That explains it then. If having those large samples is important to you and you prefer faster save times with IT/MPTM files, you can turn off sample compression by setting the two hidden settings described here to the value 0: https://forum.openmpt.org/index.php?topic=4961.0 - other formats don't have compressed samples so these settings doesn't affect them.
Sample compression can take a bit longer compared to just writing raw sample data to disk.

Alternatively if you are working with the MPTM format, you can make use of External Samples so that the sample data doesn't have to be explicitly saved to the module file every time, reducing the time it takes to save the file even further.