As the travel purpose of non-occupied taxies is to find new passengers rather than to arrive at the destination, large differences exist in the route choice behavior between the occupied and non-occupied taxies.With the assistance of geographic information system(GIS) and taxi-based floating car data(FCD), this paper investigates the behavior differences between occupied and non-occupied taxi drivers with the same origin and destination. Descriptive statistical indexes from the FCD in Shenzhen, China are explored to identify the route choice characteristics of occupied and non-occupied taxies. Then, a conditional logit model is proposed to model the quantitative relationship between drivers’ route choice and the related significant variables. Attributes of the variables related to non-occupied taxies’ observed routes are compared with the case of occupied ones. The results indicate that, compared with their counterparts, non-occupied taxi drivers generally pay more attention to choosing arterial roads and avoiding congested segments. Additionally, they are also found less sensitive to fewer traffic lights and shorter travel time. Findings from this research can assist to improve urban road network planning and traffic management.