Objective To investigate the impact of different final rinsing parameters of automated endoscopic reprocessors on peracetic acid (PAA) residuals in gastrointestinal endoscope channels, and to provide scientific evidence for optimizing endoscope cleaning and disinfection processes in clinical settings and reducing patient exposure risks. Methods From January to March 2025, 86 gastroscopes and 6 automated endoscopic reprocessors regularly used in the Endoscopy Center, Zhongshan Hospital, Fudan University were selected as the research subjects. They were divided into 3 groups based on the duration and frequency of final rinsing (group A: final rinsing for 2 times, with each rinsing lasting for 2.5 minutes, and a total rinsing time of 5 minutes; group B: final rinsing for 3 times, with each rinsing lasting for 2 minutes, and a total rinsing time of 6 minutes; group C: final rinsing for 3 times, with each rinsing lasting for 2.5 minutes, and a total rinsing time of 7.5 minutes). The PAA residuals in the endoscope channels of each group before and after drying were detected, and the compliance rates of PAA residues with standards were calculated. Results During the study period, groups A, B, and C underwent 40, 52, and 43 endoscopic disinfection procedures, respectively. Before drying, there was a significant difference in the residual PAA levels among the three groups (median PAA residual levels in groups A, B, and C were 5.34, 2.51, and 0.94 mg/L, respectively; P<0.05). Further pairwise comparisons also showed statistically significant differences (P<0.05). After drying, there was a significant difference in the residual PAA levels among the three groups (median PAA residual levels in groups A, B, and C were 3.37, 0.90, and 0.75 mg/L, respectively; P<0.05). However, further pairwise comparisons revealed no significant difference in PAA residual levels between group B and group C (P>0.05), while the remaining pairwise comparisons showed statistically significant differences (P<0.05). Within-group comparisons of PAA residual levels before and after drying showed significant differences in PAA residual levels in groups A and B before and after drying (P<0.05), while there was no significant difference in PAA residual levels in group C before and after drying (P>0.05). The PAA residual compliance rates in groups A and B after drying were significantly higher than those before drying (group A: 5.00% before drying and 27.50% after drying; group B: 1.92% before drying and 57.69% after drying; P<0.05), while there was no significant difference in the PAA residual compliance rates in group C before and after drying (P>0.05). Conclusions Increasing the number of final rinsing, extending the rinsing duration, and intensifying the drying process can effectively reduce PAA residues. Clinically, it is recommended to optimize the final rinsing parameters of the automated endoscopic reprocessor, combined with intensified drying, to reduce PAA residues and ensure patient safety.