可以同时在两个窗口上设置OpenCV鼠标回调吗?

是的,有可能:

void onMouse(int event, int x, int y, int, void* userData)
{
    int * windowID = (int*)userData;
    std::cout << "mouse in window: " << (*windowID) << std::endl;

    if((*windowID) == 1)
    {
        // do whatever you want to do for window 1
    }
    else if((*windowID) == 2)
    {
        // do whatever you want to do for window 2
    }
}

int main(int argc, char* argv[])
{
    cv::Mat input = cv::imread("C:/StackOverflow/Input/Lenna.png");

    cv::imshow("input1", input);
    cv::imshow("input2", input);

    int id1 = 1;
    int id2 = 2;
    cv::setMouseCallback("input1", &onMouse, &id1);
    cv::setMouseCallback("input2", &onMouse, &id2);

    cv::waitKey(0);
    return 0;
}