Bus passengers and cyclists often interact with each other at bus stops, which causes potential conflicts and safety risks. However, the safety impact of different types of bus stops on vulnerable road users has received limited attention. This study measures the safety impact of different types of bus stops on the interactions between passengers and cyclists. 3,136 passengers and 4,135 cyclists are observed at twelve typical bus stops in Nanjing, China. Road users’ behaviours, safety risks and congestion levels at different types of bus stops and their influential factors are analysed. Logit model and partial proportional odds model are used to analyse the occurrence rate and the severity of passenger-cyclist conflicts, respectively. Results indicate that generally floating bus stops with dedicated cycleway provide a safer environment for vulnerable road users, compared to curbside bus stops. Many factors are found increasing the safety risk significantly, including narrow road width, passengers using mobile phone, wrongful riding direction of cyclists, high passenger or cyclist densities, and passenger-cyclist interaction in cross direction. There is also a significant difference on the lag-time of road users at different types of bus stops. It is recommended that the layout design of bus stops should provide sufficient space for road users, and various regulations could be taken into consideration to alleviate the conflicts at bus stops and protect the safety of both passengers and cyclists.