This study aims to detect the levels of mucin (MUC)-4, metalloproteinase (MMP)-7, and MMP-8 in peri-implant crevicular fluid (PICF) and investigate whether the novel combinations of MMP-7 and MUC-4 are effective markers of peri-implant diseases, particularly when used in the PICF of healthy individuals, to provide a theoretical basis for finding a novel reference index that can aid the diagnosis, evaluation, and treatment of peri-implant diseases. A total of 63 subjects with 2-5 years of upper prosthesis loading were selected according to inclusion and exclusion criteria, composed of 24 controls and 39 patients with peri-implantitis (PI) group. MUC-4, MMP-7, and MMP-8 levels were detected through enzyme linked immunosorbent assay (ELISA). No significant differences in age, sex, and other parameters were found between the PI and control groups. The PI group had higher MMP-7 and MMP-8 expression levels (P<0.05) but lower MUC-4 level (P<0.001). Correlation analysis showed that MMP-7 was positively correlated with pocket probing depth (PPD) (r=0.451, P<0.001); MMP-8 was positively correlated with PPD, bleeding on probing (BOP), and gingival index (GI) (r=0.619, P<0.001; r=0.478, P<0.001; r=0.332, P=0.009). MUC-4 was negatively correlated with PPD, BOP, and GI (r=-0.492, P<0.001; r=-0.321, P=0.010; r=-0.396, P=0.001). MMP-7, MMP-8, and MUC-4 had certain diagnostic efficacy for PI. MMP-8 exhibited the best diagnostic efficacy for PI. When the cutoff value of MMP-8 was >21.21, the area under the curve (AUC) was 0.868, and the sensitivity and specificity for the diagnosis of PI were 0.96 and 0.68, respectively. The diagnostic efficacy of MMP-7 and MUC-4 parallel diagnostic models was higher than that of each factor, and the diagnostic sensitivity of the model for PI was 0.96, and the specificity was 0.56. Differences in MMP-7 and MUC-4 levels were found between the inflammation and control groups and may be diagnostic indicators for predicting PI; combinations of MMP-7 and MUC-4 had a good diagnostic value for inflammation.