MyProject
├─CMakeLists.txt
├─Main.cpp
└─SubModule
   ├─CMakeLists.txt
   ├─SubModule.cpp
   └─SubModule.h

cmake_minimum_required(VERSION 3.0)
project("C_application") 

add_executable(Main "Main.cpp")

add_subdirectory(SubModule)
target_include_directories(Main PUBLIC ./SubModule)
target_link_libraries(Main SubModule)

#include <stdio.h>
#include "SubModule.h"

int main()
{
    SubModule_funcDouble(10);
    return 0;
}

cmake_minimum_required(VERSION 3.0)
add_library(SubModule STATIC SubModule.cpp SubModule.h)

#include <stdio.h>
#include "SubModule.h"

int SubModule_funcDouble(int a)
{
    printf("SubModule_funcDouble: %d x 2 = %d\n", a, a * 2);
    return a * 2;
}

#ifndef _SUB_MODULE_H_
#define _SUB_MODULE_H_

#ifdef __cplusplus
extern "C" {
#endif
#if 0
}
#endif

int SubModule_funcDouble(int a);

#ifdef __cplusplus
}
#endif

#endif  /* _SUB_MODULE_H_ */

MyProject
├─AndroidApp/     <-- ここにAndroidプロジェクトを保存
├─CMakeLists.txt
├─Main.cpp
└─SubModule/
   ├─CMakeLists.txt
   ├─SubModule.cpp
   └─SubModule.h

~略~

add_library( # Sets the name of the library.
        native-lib

        # Sets the library as a shared library.
        SHARED

        # Provides a relative path to your source file(s).
        native-lib.cpp)

find_library( # Sets the name of the path variable.
        log-lib

        # Specifies the name of the NDK library that
        # you want CMake to locate.
        log)

~略~

target_link_libraries( # Specifies the target library.
        native-lib

        # Links the target library to the log library
        # included in the NDK.
        ${log-lib})

# ↓追加
add_subdirectory(../../../../../SubModule SubModule)
target_include_directories(native-lib PUBLIC ../../../../../SubModule)
target_link_libraries(native-lib SubModule)
# ↑追加

#include <jni.h>
#include <string>

extern "C" JNIEXPORT jstring JNICALL
Java_com_example_myapplication_MainActivity_stringFromJNI(
        JNIEnv *env,
        jobject /* this */) {
    std::string hello = "Hello from C++";
    return env->NewStringUTF(hello.c_str());
}

// ↓追加
#include "SubModule.h"
extern "C" JNIEXPORT jint JNICALL
Java_com_example_myapplication_MainActivity_funcDouble(
        JNIEnv *env,
        jobject /* this */,
        jint a
) {
    int ret = SubModule_funcDouble(a);
    return ret;
}
// ↑追加

package com.example.myapplication;

import android.support.v7.app.AppCompatActivity;
import android.os.Bundle;
import android.util.Log;
import android.widget.TextView;

public class MainActivity extends AppCompatActivity {

    // Used to load the 'native-lib' library on application startup.
    static {
        System.loadLibrary("native-lib");
    }

    @Override
    protected void onCreate(Bundle savedInstanceState) {
        super.onCreate(savedInstanceState);
        setContentView(R.layout.activity_main);

        // Example of a call to a native method
        TextView tv = findViewById(R.id.sample_text);
        tv.setText(stringFromJNI());

        // ↓追加
        int ret = funcDouble(10);
        Log.i("MyApp", "funcDouble: " + ret);
        // ↑追加
    }

    /**
     * A native method that is implemented by the 'native-lib' native library,
     * which is packaged with this application.
     */
    public native String stringFromJNI();

    // ↓追加
    public native int funcDouble(int a);
    // ↑追加
}

# ↓追加
find_package(OpenMP REQUIRED)
if(OpenMP_FOUND)
    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
endif()
# ↑追加

add_subdirectory(../../../../../SubModule SubModule)
target_include_directories(native-lib PUBLIC ../../../../../SubModule)
target_link_libraries(native-lib SubModule)