This research explores the application of available information from Automated Data Collection Systems (ADC) with a focus on bus passenger Origin-Destination (OD) matrices inference, using Chongqing as a case study. It demonstrates the feasibility and ease of applying to infer bus passengers boarding and alighting locations if boarding information is available from neither Automatic Fare Collection System (AFC) nor GPS data, and is the first known attempt to create an algorism to use stop Geographic Information System (GIS) and dual-direction bus stop group to estimate the boarding location and traveling direction when GPS data cannot provide the arriving information at bus stops. The results of this research have been practically applied to a full-size bus network in Chongqing, and can be easily implemented to other Chinese cities as Chongqing presents most popular data structure of ADC in China.