In a quadcopter, a navigation system is needed to monitor the position and control the movement of the quadcopter. In recent years, a navigation system based on longitude and latitude coordinates has been developed, namely a waypoint system. This flight control system works to maintain the actual position and direction of the quadcopter to its destination. Thus, the authors designed a navigation control system using the waypoint method on a quadcopter which can walk autonomously from one coordinate point to another coordinate point or destination. This navigation system works using GPS (Global Positioning System), and GY-81 as a magnetometer sensor. The application of the waypoint method can help the robot to determine the direction toward the destination and how far the target is from the robot's current position. This is evidenced in the movement of the robot with an accuracy value of up to 99.48% and an average time to reach the target in about 50-65 seconds. The application of the PID method gives better heading results compared to those without using the PID method. This is evidenced by the stable robot movement and fairly accurate compass sensor readings. Based on the test results using the PID method on the seacoast, the error = 2.15% and the accuracy = 97.85%, while in the test without the PID method on the land surface, the error = 3.33% and the accuracy = 96.6%. For testing using the PID method in paddy fields, an error result = 1.85% and an accuracy result = of 98.1%, while testing without the PID method on the surface of the water obtained an error result = 2.75% and an accuracy result = 97.25%.