Objective: To analyze the histopathological characteristics of peri-implant soft tissue in reconstructed jaws and the changes after keratinized mucosa augmentation (KMA) with free gingival graft (FGG). Methods: Twenty patients were enrolled in this study. Five patients of them, who were periodontal and systemic healthy and referred for crown lengthening before restoration with healthy keratinized gingiva collected were enrolled as healthy controls. 15 patients of them were with fibula or iliac bone flaps jaw reconstruction (10 with fibula flap and 5 with iliac flap), who were referred to FGG and implant exposures before restoration. Soft tissue was collected before FGG in reconstructed jaws, and in 5 patients (3 with fibula flap and 2 with iliac flap) 8 weeks after FGG if a second surgery was conducted. Histological analysis with hematoxylin-eosin stain and immunological analysis to interlukin-1 (IL-1), interlukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) were performed. Results: Thickness from the bottom of stratum basale to the top of stratum granulosum and thickness of keratinized layer in reconstructed jaws were significantly lower compared with that of natural healthy keratinized gingiva [0.27 (0.20, 0.30) mm vs. 0.36 (0.35, 0.47) mm, P<0.05; 16.49 (14.90, 23.37) μm vs. 26.37 (24.12, 31.53) μm, P<0.05]. In the reconstructed area, thickness from the bottom of stratum basale to the top of stratum granulosum increased after KMA with FGG [0.19 (0.16, 0.25) mm vs. 0.38 (0.25, 0.39) mm, P=0.059] and the thickness of keratinized layer significantly increased after KMA with FGG [16.42 (14.16, 22.35) μm vs. 28.57 (27.16, 29.14) μm, P<0.05], which was similar to that in the control group. Furthermore, the number of positive cells of IL-1, IL-6 and TNF-α significantly increased after KMA [0.67 (0.17, 8.93) vs. 11.00 (9.16, 18.00); 13.00 (8.50, 14.14) vs. 21.89 (15.00, 28.12); 0.22 (0.04, 0.63) vs. 2.83 (1.68, 5.00), respectively, P<0.05] as well as the average optical density value [0.15 (0.14, 0.17) vs. 0.18 (0.17, 0.21); 0.28 (0.26, 0.33) vs. 0.36 (0.33, 0.37); 0.23 (0.22, 0.29) vs. 0.30 (0.28, 0.42), respectively, P<0.05], which was similar to that in the healthy keratinized gingiva. Conclusion: The lack of rete pegs and inflammatory factors were common in soft tissue with jaw reconstruction. FGG can improve the quality of the epithelium and may improve the stability of the mucosa around implants.