Implants with platform-switching (PS) design have been demonstrated to reduce marginal bone loss. However, the influence on peri-implant soft tissue healing is unclear. This study was designed to investigate its effect on peri-implant soft tissue healing after implant uncovery. Non-smokers needing two implants in different quadrants were recruited in this study. For each individual, one PS and one platform-matching (PM) implants were placed using two-stage protocol. Following 2 to 8 months of healing, all implants were uncovered and connected to the corresponding healing abutments. Clinical measurements and peri-implant crevicular fluid (PICF) were taken at 1-, 2-, 4-, and 6-week after 2nd stage surgery. The cytokine concentrations in PICF were analyzed. Peri-implant mucosa (1 × 2 × 2mm) was harvested around the healing abutment for the analysis of gene expression at uncovery and 6-week post-uncovery. Eighteen participants (nine males; 51.7 ± 14.9 years) were recruited. Compared to PM, PS showed significantly lower probing depth (PD) at 1- and 2-week as well as modified sulcus bleeding index (mSBI) at 1-, 4-, and 6-week (P<0.05). Over time, a decrease in osteoprotegerin and interleukin-1β concentrations in PICF along with an increase in receptor activator of unclear factor kappa-B ligand, periostin, and peroxidasin gene expressions in peri-implant mucosa were noted within both groups (P<0.05) without significant intergroup differences. Within the limits, implants with PS design rendered significant benefits over PM design in PD and mSBI reduction during a 6-week healing. However, molecular changes within PICF and peri-implant mucosa as a response to PM and PS appear negligible.