PX4-Autopilot

I am working on simulation and how can ı use PX4-Autopilot with my custom catkin_workspace ?

Your question is not very clear, but I think that you want to get data from simulation (drone data) and make something in your own ROS package based on this data, right ?
You can refer to this link:
https://docs.px4.io/master/en/simulation/ros_interface.html