As three-dimensional printing (3DP) technology continues to develop, it has successfully prepared rock mass samples repetitively and reproducibly. Previous studies primarily focused on comparing the mechanical properties and the pore structure between 3DP rocklike samples and natural rocks based on traditional uniaxial compression and CT scanning tests at single-stress conditions. In this study, 3DP gypsum samples were prepared for uniaxial compression tests equipped with the high-resolution in situ X-ray micro-computed tomography (Micro-CT) apparatus to obtain two-dimensional (2D) Micro-CT scanning images of 3DP gypsum samples at different stages of deformation. Based on the Micro-CT images, the cracking and pore structure evolution of 3DP gypsum samples were quantitatively analyzed. Results indicate that as the load increases, the void ratio of 3DP gypsum samples first decreases gradually and then increases slowly, which is later followed by a rapid rise along with failure. The cracks could be categorized into three types based on their initiation and growth mechanism: cracks that initiate and grow along the interface (Crack I), pores (Crack II), and residual binders (Crack III). Compared with pores in the compression region, pores were more prone to connect with adjacent pores in the extension region, forming larger pores. The qualitative and quantitative results are essential to characterizing and understanding the failure mechanism and microstructural evolution of 3DP gypsum samples for modeling natural rock behavior. 3DP technology, with its highly customizable and precisely controllable features, presents an innovative approach for the fabrication of rock analogs. Currently, a topic of considerable debate revolves around the efficacy of utilizing 3DP as a viable replacement for natural rocks. To address this issue, we conducted an investigation into the cracking mechanisms and pore evolution of 3DP rocks under in situ compression experiments. First, we investigated the particle size distribution and composition of ZP150 powder. Subsequently, 3DP gypsum samples were manufactured using the ZPrinter 450 using ZP150 powder and Zb63 binder as the printing materials in this study. By complying with an in situ Micro-CT scanner, we conducted a microscopic investigation of crack behavior and pore evolution in the 3DP gypsum samples during uniaxial compression experiments. Through comprehensive analysis of visualized cracks and pores, a novel failure mode of 3DP gypsum samples under loading was proposed, considering the impacts of pores, bedding planes, and residual binder. The results presented in this study are important for characterizing and understanding the failure mechanism and microstructural evolution of 3DP gypsum samples when modeling natural rock behavior or conducting physical model experiments.