Spatial distribution orientations of blocks can cause significant errors in the discrete element model (DEM) calculation of soil-rock mixture (SRM). To avoid this error, spherical harmonic (SH) series whose harmonization degrees fixed at 15 were proposed for block reconstruction. This research refers to the case-history of a deep excavation rift valley spanning from the Mabian to Zhaojue section of the Leshan-Xichang Expressway, mainly containing moderately-weathered silty mudstone, in the Leshan City, Sichuan Province, China. The appropriate degree of finite-term SH series is selected by the volume, surface area. 100 blocks were scanned on site, and sphericity and angularity of the blocks were calculated. The sphericity and angularity of 50 reconstructed blocks were considered for the error analysis of SH method. Moreover, stochastic polyhedron method was considered for comparing different block reconstructions. The maximum block placement angle was defined to control the spatial distribution orientations of the blocks. Large scale direct tests were carried. Numerical simulations of large-scale direct shear tests were conducted to study the influence of the spatial distribution orientations of the blocks on the mechanical properties of the SRMs. The results revealed that the finite-term SH series fixed at 15 accurately reflected the shape characteristics and mechanical behaviors of actual blocks. The spatial distribution orientations of the blocks had a minimal impact on the friction angle and cohesion of SRM constructed through the SH method. The SRMs developed via the SH method exhibited marginal variations in contact force and anisotropy index of contact across diverse block placement strategies. The evolution of coordination number was closer when employing the SH method under varied block placement methods. Blocks reconstructed by the SH method, could mitigate errors in DEM calculation caused by the spatial distribution orientations of the blocks.