In order to investigate the key factors influencing over-under-excavation in multi-jointed rock mass tunneling with shaped charge blasting, the finite element numerical simulation and orthogonal test method were used. Six factors, including joint spacing, joint number, joint dip angle, joint thickness, in-situ stress, and borehole spacing, were comprehensively considered to study their effects on the over-under-excavation volume. Range analysis was then employed to determine the main controlling factors. The results show that in-situ stress, borehole spacing, and joint dip angle are the primary factors causing over-under-excavation. When the in-situ stress is 4 MPa, the damage range of the surrounding rock is relatively small and crack propagation between boreholes can be ensured. Borehole spacings of 60 cm or 80 cm can effectively control the occurrence of over-under-excavation. A larger joint spacing is conducive to the directional propagation of blasting cracks, thereby significantly optimizing the over-under-excavation control effect. It is concluded that this study can provide a reference for shaped charge blasting construction in multi-jointed rock masses, offering guidance for optimizing blasting parameters, improving blasting methods, and forming good blasting contours.