This study investigated the inflammatory effect of intraoperative mitomycin C (MMC) on adhesion reformation in human rectus muscles. Ten consecutive patients who underwent medial rectus resection had their postoperative rectus muscles divided into two groups: control group (n = 10) and MMC group (n = 10). In the MMC group, the muscle was soaked for 2 min with MMC, prepared as a 0.2 mg/mL (0.02%) solution. The 0.02% MMC reactions were examined using histological analysis with hematoxylin-eosin (inflammatory response) and Masson's trichrome (collagen fibrils), immunoreactivities of cyclooxygenase-II (inflammatory response), and collagen type I and III, scanning electron microscopy analysis to quantify the diameter and D-periodicity of collagen fibrils, and atomic force microscopy analysis to quantify the diameter, D-periodicity, and adhesion force of collagen fibrils. The rectus muscles treated with 0.02% MMC showed a significantly increased inflammatory response (p < 0.05), increased collagen density (p < 0.0001), increased fibril diameter (p < 0.001 or p < 0.05), and decreased fibril adhesion force (p < 0.005) compared to the rectus muscles in the control group. MMC simultaneously caused an inflammatory response as well as nanostructural and biomechanical property changes in the collagen fibril network.