The device of the research of mechatronic complex for detection, fixation, storage of mobile objects, its structure and the principle of action are presented in the article. The main components of the mechatronic complex are: pneumatic actuators controlled by Siemens S7-1200 programmable logic controller; the system for detecting moving objects and controlling the movement of actuators in real time, consisting of magnetic position sensors and an optical sensor. There are problems in the automatic control mode of the mechatronic complex. It is necessary to determine the balance between minimum time for combining the axes of a moving object and pneumatic actuators and delay time for implementing a command to fix a moving object. These process variables are controlled by system delay timers. Thus, the technological operation of fixing a moving object is the most complicated operation in the mechatronic complex for programming. The authors have developed mathematical methods and software to solve problems of combining the axes, allowing to synchronize technological operations in two modes. The kinematic model of the mechatronic complex, which allows to determine delay time for fixing a moving object, is presented. The sequence of movements of the actuator mechanisms, depending on the signal states of the optical and magnetic position sensors, is depicted as a cyclogram and implemented in the language of relay-contact circuits. Usage of system timers in the structure of the software code, which ensure the combination of axes of pneumatic capture and the moving object, is the main feature of the mechatronic complex. Experimental results show an improvement in reliability and speed when mechatronic complex works in the automatic control mode.