Understanding the spontaneous imbibition in the natural fracture with heterogeneous wettability is crucial for predicting and mitigating the impacts of unstable displacement on unconventional recovery. In this paper, the fracture structured mesh model is reconstructed based on the micro-computed tomography (micro-CT) image of naturally fractured tight sandstone. The mineralogy map-based modeling method for heterogeneous-wetting fracture is developed by combining the thin section images, X-ray diffraction (XRD) analysis, and multiple point statistics method. The simulation of the single-phase flow is performed to test the mesh independence. The effects of gravity and wettability on spontaneous imbibition in natural fracture and corresponding imbibition front dynamics are analyzed and discussed using the volume of fluid (VOF) method. The results show that (1) The structured mesh reconstruction method proposed in this paper can more effectively preserve the fracture structure compared to the unstructured mesh reconstruction method. (2) Gravity has a negligible impact on the pore-scale spontaneous imbibition in natural fracture. Under homogeneous-wetting conditions, spontaneous imbibition in natural fracture consistently exhibits stable displacement without significant residual gas formation. However, under the heterogeneous-wetting condition, the spontaneous imbibition displays typical capillary fingering, resulting in approximately 24.04% of the gas being trapped after spontaneous imbibition. The residual gas trapping mechanisms mainly include adhered, isolated, and connected gas. (3) Under both homogeneous- and heterogeneous-wetting conditions, the imbibing water saturation and the length of the imbibition front are proportional to the power of imbibition time during spontaneous imbibition in the natural fracture.