The preservation and restoration of heritage sites have always been of key focus in the field of cultural relics. Current restoration methods mainly involve physical or chemical techniques, which are in many cases intrusive, destructive, and irreversible. Hereby, we introduce a novel biological strategy (microbial-induced carbonate precipitation (MICP)) to repair natural and simulated surface cracks on six hundred years’ old wall bricks (part of the Nanjing City Min Dynasty ancient wall, China). X-ray micro computed tomography (X-ray micro-CT) was employed to non-destructively visualize the internal structure of the MICP-treated brick cubes. The results showed that MICP can effectively repair both natural and simulated cracks present on the brick’s surface. The compressive strength of the MICP-treated brick cubes was significantly higher than that of the untreated control cubes (33.56 ± 9.07 vs. 19.00 ± 1.98 kN, respectively). MICP significantly increased the softening coefficient and decreased the water absorption rate (p < 0.05), indicating that the water resistance of the wall bricks can be improved after treatment. The 3D images from X-ray micro-CT, a method that could non-destructively assess the internals of such cultural structures, showed that MICP can effectively repair ancient relics, promoting durability and limiting degradation without affecting the structure. X-ray diffraction analyses showed that MICP generates the same calcite form as that of original bricks, indicating that MICP filler is compatible with the ancient city wall brick. These findings are in line with the concept of contemporary heritage preservation.