In this paper, Petri Nets tool is used to model logical operations, faults detection, controller designed and consequently significant growth in reliability for electromechanical actuator subsystem of UAV. In UAVs, actuators are used to control surfaces, therefore introducing a new way that can simulate the logical behavior and subsystem fault and control the system’ s probable errors, is beneficial. To design a controller based on Petri Nets, three stages have to be done; in the first stage, different sections and main features are modeled using Petri Nets. In the second stage, synchronization is done among resulted models, then using supervisory control in the third stage, in order to ensure the unsafe situation occurrence in the system, the all control procedure is guaranteed. In this research, analytical redundancy is used to prevent entering into unsafe conditions and process control. Results show that by using this method, the probability of fault detection increases and consequently the reliability has the same faith.