An integrated navigation system aims to deal with autonomous navigation, positioning, motion control, and equipment calibration, generally combining two or more navigation devices on carriers. In this study, an intelligent integrated navigation system was therefore designed for agricultural machinery using Global Navigation Satellite System (GNSS) and Inertial Navigation System (INS), in order to improve the positioning accuracy and reliability of automatic navigation in agricultural machinery. The system was derived from the angular velocity and acceleration of INS three-axis attitude, as well as the position and velocity of high-precision positioning board. The loose-coupling mode and real-time correction of INS error were adopted via a Kalman filter to collect the accurate position, velocity and attitude of agricultural machinery. The automatic navigation of agricultural machinery reduced labor intensity and costs for better profits, despite being one of the key technologies for the development of modern agriculture. Most automatic navigation of agricultural machinery currently used the GNSS and INS for positioning and navigation. But there is still a great challenge on some defects, such as the lack of GNSS signals, and the accumulation of INS errors over time. A control board of intelligent agricultural machinery was also manufactured to integrate the GNSS high-precision analysis and inertial measurement, where the integrated navigation program was implemented. The specific procedure was as follows. 1) To determine the project implementation plan and related devices; 2) To design an integrated navigation system, including the structure and mode of GNSS/INS, where the loose coupling mode was set; 3) To design hardware circuits in the PCB production and develop software program in C language under Keil5 IDE; 4) To test the positioning and navigation effects of the system in actual farmland and further verify the accuracy and stability of positioning and navigation system. In addition, a test platform of DF1004-2 intelligent agricultural machinery was established to perform in the Beidou field under static and linear motion. A comparison was also made on the single GNSS and combined navigation. The test results showed that there was little difference in the performance between single GNSS and integrated navigation, where the positioning error was less than 1 cm, and the attitude angle error was less than 0.1°, when the agricultural machinery was stationary. The system output simultaneously single GNSS and GNSS/INS integrated navigation information, when the agricultural machinery was driven in a preset straight path at a speed of 2 m/s. The position error of single GNSS navigation was less than 6 cm, and the attitude angle error was less than 1°, whereas, the position error of GNSS/INS integrated navigation was less than 3 cm, and the attitude angle error was less than 0.5°. There was a limited gain that was provided by the inertial measurement under stationary conditions, due to the zero-moving speed, in line with the theory of dead reckoning. In the case of movement, the GNSS/INS integrated navigation presented a greater accuracy than single GNSS navigation. The finding can provide strong support to high precision and automatic navigation control of machines in intelligent agriculture.