I have an android project created by Android Studio 2.2.3 under Windows 10, this project use a native library through its wrapper jar (through JNI). The native library was built
How do you expect the AndroidStudio to hit your breakpoint if your program is running over the pre-compiled code? It would be the same if you put a breakpoint in the source-code say in your Notepad++ application. Instead, you have to tell your project/code to use the source-code and not the pre-compiled lib. For this, remove all the .so files and link the source-code so NDK will compile from there.