Drones have been quickly developing for civilian applications in recent years. Because of the nonlinearity of the mathematical drone model, and the importance of precise navigation to avoid possible dangers, it is necessary to establish an algorithm to localize the drone simultaneously and maneuver it to the desired destination. This paper presents a visual-based multi-stage error tolerance navigation algorithm of an autonomous drone by a tag-based fiducial marker detection in finding its target. Dynamic and kinematic models of the drone were developed by Newton-Euler. The position and orientation of the drone, related to the tag, are determined by AprilTag, which is used as feedback in a closed-loop control system with an Adjustable Proportional-Integral-Derivative (APID) controller. Parameters of the controller are tuned based on steady-State error, which is defined as the distance of the drone from the desired point. The sequence of path trajectory, that drone follows to reach the desired point, is defined as a navigation algorithm. A model of the drone was simulated in a virtual outdoor to mimic hovering in complex obstacles environment. The results present satisfactory performance of the navigation system programmed by the APID controller in comparison with the conventional Proportional-Integral-Derivative (PID) controller. It can be ascertained that the proposed navigation system based on a tag marker in the closed-loop control system is applicable to maneuvering the drone autonomously and useful for various industrial tasks in indoor/outdoor environments.