Simultaneous localization and mapping (SLAM) is one of the key technologies for agricultural robots to build maps and localize in complex orchard environments and realize unmanned autonomous operations. Due to the complexity of the orchard environment, the single canopy feature and the diffuse reflection of light caused by the leaves, etc., the map construction process of the orchard environment leads to mismatch and increases the cumulative error of the map construction. Aiming at the above problems, this paper propose a navigation map construction method for orchard environment based on the fusion of Scan Context and NDT-ICP. The method firstly searches the Ring key quickly to get the candidate frames, and scores the similarity between the candidate frames and the current frame, and effectively detects the loopbacks by two-stage searching algorithm to reduce the false matches in the map of orchard environment. Meanwhile, a point cloud alignment method based on the fusion of normal distribution transform coarse alignment and iterative nearest point exact alignment is used to reduce the cumulative error of the orchard environment map. The results show that the improved algorithm compensates the drift of the point cloud map with higher mapping accuracy, better real-time performance, lower resource utilization, higher overlap between the trajectory estimation and the real trajectory, smoother loops, and a 4% reduction in CPU occupancy. In the complex orchard environment, the root mean square error and standard deviation of the trajectories of this paper's algorithm are 0.57 m and 0.19 m, which are 68% and 83% higher than those of the loop detection algorithms in the Lightweight Ground Optimized Lidar Trajectory Measurement and Multivariate Terrain Mapping (LeGO-LOAM), respectively. Accurate map construction and low drift pose estimation can be performed.The research algorithm effectively reduces the influence of mis-matching and large cumulative error in the process of map construction in the orchard environment, meets the demand for high-precision environmental mapping in the orchard environment, and provides technical support for promoting unmanned operation in the orchard environment.