You can't cross compile with just a flip of a switch. QB64 has a lot of distinct commands which translate completely into utterly different c-code depending on your operating system.
With Linux, you should be able to download a standard 32-bit version of QB64, and run it inside WINE to produce 32-bit Windows EXEs.
Even easier than that: Install Windows in a Virtual Machine, put QB64 in it, and compile there.
(For example, take the CONSOLE commands... Those all rely on native windows API calls. There's no simple Linux substitute for them, so you're not going to set a -windows flag to toggle over from the X11 calls and such for them.)