Accurate positioning at the inter-row canopy can provide data support for precision variable-rate spraying. Therefore, there is an urgent need to design a reliable positioning method for the inter-row canopy of closed orchards (planted forests). In the study, the Extended Kalman Filter (EKF) fusion positioning method (method C) was first constructed by calibrating the IMU and encoder with errors. Meanwhile, 3D Light Detection and Ranging (LiDAR) observations were introduced to be fused into Method C. An EKF fusion positioning method (method D) based on 3D LiDAR corrected detection was designed. The method starts or closes method C by the presence or absence of the canopy. The vertically installed 3D LiDAR detected the canopy body center, providing the vehicle with inter-row vertical distance and heading. They were obtained through the distance between the center of the body and fixed row spacing. This can provide an accurate initial position for method C and correct the positioning trajectory. Finally, the positioning and canopy length measurement experiments were designed using a GPS positioning system. The results show that the method proposed in this study can significantly improve the accuracy of length measurement and positioning at the inter-row canopy, which does not significantly change with the distance traveled. In the orchard experiment, the average positioning deviations of the lateral and vertical distances at the inter-row canopy are 0.1 m and 0.2 m, respectively, with an average heading deviation of 6.75°, and the average relative error of canopy length measurement was 4.35%. The method can provide a simple and reliable inter-row positioning method for current remote-controlled and manned agricultural machinery when working in standardized 3D crops. This can modify the above-mentioned machinery to improve its automation level.