The irregularity and complexity of formation fracture morphology lead to great uncertainty in lost circulation control. At present, the fracture morphology is simplified to be smooth in the process of fracture plugging investigation, thus the influence of fracture surface morphology on the retention behavior and pressure bearing capacity of granular lost circulation materials (LCMs) remains unknown. To fill this gap, the reverse engineering technology was utilized for investigating the influence of fracture surface morphology on plugging performance. In this study, the three-dimensional (3D) reverse reconstruction and quantitative characterization of fracture surface were realized based on the 3D coordinates of real fracture surfaces, which were obtained through the 3D structured light scanning. A new parameter “particle size matching factor” was established to analysis the retention behavior of LCM particles. A new method for fracture plugging experiments was established based on 3D printing technology, which can obtain the structure of the sealing zone in fracture with real morphology. The results show that the irregularity of the real fracture surface leads to the local shrinkage of the flow channels, while provide support force to LCMs, which has an important influence on the plugging performance of LCMs. The larger the “particle size matching factor”, the easier to form retention in fractures. With the increase of Joint Roughness Coefficient (JRC) and fractal dimension, the pressure bearing capacity of the sealing zone is significantly improved. The research results are helpful to more accurately realize the plugging mechanism of granular LCMs, which contributes to improve efficiency of lost circulation control.