To improve the endurance limits of triply periodic minimal surface (TPMS)-based scaffolds, the post-treatment process combing hot isostatic pressing (HIP) and electropolishing (ELP) was proposed and conducted in TPMS-based scaffolds with various structures. Thus, the fatigue properties were enhanced from three aspects: changing the topological structures of TPMSs, improving surface qualities and eliminating internal defects. The stretching-dominated scaffold-new diamond (AD) and the bending-dominated scaffold-network-based gyroid (IG) were selected and their relative densities were set to 20%. These scaffolds were fabricated by electron beam melting using Ti6Al4V powders. HIP and ELP were conducted in the manufactured scaffolds. Then, compression–compression fatigue tests were performed and fatigue parameters such as fatigue life, accumulated strain rate, fatigue strength and fatigue ratio were obtained. The experimental techniques of scanning electron microscopy, microcomputer tomography, optical microscopic, X-ray diffraction and electron backscattered diffraction were carried out to characterise the surface qualities, internal defects and microstructures. The effects of topological structure and surface quality on the stress distribution on TPMS-based scaffolds under compressive loading were investigated by finite element analysis. Results show that topological structures, surface qualities and internal defects all affect the fatigue properties of TPMS-based scaffolds. Under cyclic compressive loading, the fatigue ratios of IG and AD without undergoing post-treatment are 0.11 and 0.59, respectively, while they rise to 0.26 and 0.69 after HIP and ELP. Compared with surface qualities and internal defects, topological structures influence the fatigue properties of TPMS-based scaffolds more prominently. The fatigue properties of TPMS-based scaffolds can be enhanced by the post-treatment process combing HIP and ELP, and greater improvement will be obtained for bending-dominated structures than stretching-dominated structures. Thus, manipulating the topological structures and increasing the buckling components of TPMS-based scaffolds is an effective way to obtain porous scaffolds with excellent fatigue properties under cyclic compressive loading. HIP and ELP can also be adopted to further improve their fatigue lives. The novelty of this study lies in improving the fatigue properties of TPMS-based scaffolds from the three aspects, which are changing the topology structure, improving the surface quality and reducing the internal defects, and the mechanisms of improving the fatigue properties of TPMS-based scaffolds are systematically discussed.