In order to realize agricultural machinery automatic navigation control, and taking into account the system cost and operation efficiency, the automatic navigation control decision method was studied, and a navigation software system was designed and developed. Firstly, the system conducted path planning according to the field boundary, the field shape and working requirements. Secondly,the simplified two-wheel vehicle kinematic model was used and the fuzzy control was adopted for navigation control decision. And the input parameters of the fuzzy controller were the lateral deviation and the heading deviation of agricultural machinery, and the output parameter was the steering angle data. Finally, using the steering angle data, the machine was controlled by the steering wheel through PLC controller. The modular design ideas were adopted in software development. The software mainly consisted of four modules: serial data communication, data analysis and processing, data and graphic display and data storage. It was developed based on C++/MFC programming language. The software can analyze and process the received data, such as GNSS positioning data, angle sensor data, attitude sensor data and PLC controller data, then send the corresponding control decision information to the PLC controller. In addition, the system can store the deviation data for error analysis after the navigation. The experimental results demonstrated that the automatic navigation control decision method can achieve preferable control precision. The software has user-friendly interface, stability communication and relatively complete function, so that the proposed automatic navigation control decision and software system can meet the field operation requirements for agricultural machinery.