Autonomous driving technology for agricultural machinery can maximise crop yield, reduce labour costs, and alleviate labour intensity. In response to the current low degree of automation and low tracking accuracy of driving paths in agricultural equipment, this research proposes an unmanned agricultural machinery operating system based on an improved fuzzy adaptive PD control algorithm. Firstly, mechanical kinematic models and fuzzy adaptive control algorithms are introduced to achieve autonomous driving, and parameter settings and speed adjustments are made while considering errors. Secondly, in the autonomous driving operation system, taking a certain rice machine as an example, perception information, trajectory design, dynamic control, operation supervision, and remote control design are carried out. The experimental results show that the improved fuzzy algorithm exhibits smaller deviation results in driving path tracking, with an average error between the actual path and the expected path of less than 0.001 m. In different testing scenarios, compared with the actual control results, the maximum deviation of the control system platform in straight sections is less than 2.8 m, which is more stable. More than 95% of the lateral deviation results in the road sections are within 0.11 m. And the tracking distance error of the proposed method in the straight and curved segments is relatively small, far smaller than other comparative algorithms. The unmanned agricultural machinery operation system proposed in this study can significantly improve the efficiency and accuracy of agricultural machinery work, promote the development of intelligent and modern agricultural machinery, and provide reference value and important contributions to social and economic development as well as the progress and promotion of related technologies.