This paper presents a newly developed 3-Dimensional (3-D) simulation system for Moving Mask Deep X-ray Lithography (M²DXL) technique, and its validation. The simulation system named X-ray Lithography Simulation System for 3-Dimensional Fabrication (X3D) is tailored to simulate a fabrication process of 3-D microstructures by M²DXL. X3D consists of three modules: mask generation, exposure and resist development (hereafter development). The exposure module calculates a dose distribution in resist using an X-ray mask pattern and its movement trajectory. The dose is then converted to a resist dissolution rate. The development module adopted the "Fast Marching Method" technique to calculate the 3-D dissolution process and resultant 3-D microstructures. This technique takes into account resist dissolution direction that is required by 3-D X-ray lithography simulation. The comparison between simulation results and measurements of "stairs-like" dose deposition pattern by M²DXL showed that X3D correctly predicts the 3-D dissolution process of exposed PMMA.