Potential users sometimes ask us if there is an iGMT version for the Microsoft Windows operating system. There is not as such, and we do not have any personal experience trying to port iGMT to Windows. However, we have gotten reports that it is not that hard to install iGMT under Windows using UNIX emulators such as cygwin or interix as "long as the user has the X-Win emulator runing and the wish_cmd is well declared." (J Luis).
Questions on how to install GMT and other required tools before trying to get iGMT to run under Windows using aforementioned emulators are discussed in the GMT FAQ. It might also be useful to do a

Especially Matlab users running Windows can also consider a recently released GMT GUI, M_GMT by J Luis. There is also a standalone version of this software that does not rely on Matlab. We have no experience with this code but it seems very useful.

Another option might be to use Win4GMT which is a GUI for GMT that runs under Windows. However, it seems that you can't obtain the source code for Win4GMT and it's built using proprietary tools. Again, we also have no experience running that software and don't know about its features.