College students are the engine of the sustainability of the future, and their awareness of environmental protection and waste classification is very important for the sustainable implementation of urban solid waste separation projects. Chongqing is one of the first 46 waste separation pilot cities in China. The primary objective of this study was to investigate the municipal waste separation behavior of college students and its influencing factors. Data from a total of 814 questionnaires among college students from sixteen universities in Chongqing were collected. Results showed that most college students think it is necessary to separate waste, and they have executed it in their daily life. Students have a high accuracy in classifying perishable waste, but they are not familiar with the classification of waste lamps, bulbs (14.00%), expired drugs (30.71%), toilet paper (11.3%), peel (18.80%) and brick kilns (27.76%). Special attention should be paid to distinguishing recyclables and other wastes. The principal factors that affect students’ willingness to classify waste are attitude, situational factors and publicity and education, which are embodied in students’ attitude towards waste separation, the surrounding environmental hygiene, the convenience of waste separation, the ease of understanding of waste separation marks and the degree of publicity and education of the school. Four measures are recommended for improving students’ willingness to separate municipal waste based on this investigation.