With increasing traffic demand in urban areas of metropolises, many tunnels have been constructed to improve road capacity and traffic mobility. The distance between two consecutive tunnels is relatively short which usually forms a weaving section, leading to considerable traffic conflicts. The objective of this study is to evaluate the safety performance of such inter-tunnel sections. Conflict prediction models based on negative binomial regression were developed to identify influential factors. Field data were collected at ten selected sites in Nanjing, China, and used for calibrating and validating the proposed models. Two types of inter-tunnel weaving sections (type 1 and type 2) were found in the field with distinct lane markings and operation rules. The unique lane markings in type 1 weaving sections are designed to isolate weaving traffic flows and thus reduce conflicts, but in practice, contradictory to its design intention, lead to more traffic conflicts compared with type 2 weaving sections. In addition, the length of the diverging section, merging section, and whole weaving section are found to be significant influencing factors on the conflict occurrence. The findings in the present study are expected to help engineer better design inter-tunnel sections.