Rice is the predominant grain crop in China, with its consumption showing a steady annual increase. Due to the diminishing labor force, China’s rice cultivation industry faces significant challenges and has an urgent requirement for automated rice transplanters. This study developed an agricultural navigation system integrating mechatronic-hydraulic control with navigation technologies to automate the rice transplanter’s driving and operational processes. The designed automation devices enable precise control over functions such as steering and working clutch. A path planning methodology was proposed to generate straight-line reference paths by giving target points and to determine the headland turning pattern based on the working width and turning radius of the rice transplanter. Additionally, an operational control strategy based on the finite state machine (FSM) was developed, enabling effective switching of the rice transplanter’s operational states through the designation of key points. The test results showed that the maximum lateral error of the rice transplanter along straight-line paths was 4.83 cm on the cement pavement and 6.30 cm in the field, with the maximum error in determining key points being 7.22 cm in the field. These results indicate that the agricultural navigation system developed in this study can achieve the automation of rice transplanters and provide certain inspiration for the research of autonomous agricultural vehicles.