Identifying traffic congestion accurately is crucial for improving the expressway service level. Because the distributions of microscopic traffic quantities are highly sensitive to slight changes, the traffic congestion measurement is affected by many factors. As an essential part of the expressway, service areas should be considered when measuring the traffic state. Although existing studies pay increasing attention to service areas, the impact caused by service areas is hard to measure for evaluating traffic congestion events. By merging ETC transaction datasets and service area entrance data, this work proposes a traffic congestion measurement with the influence of expressway service areas. In this model, the traffic congestion with the influence of service areas is corrected by three modules: 1) the pause rate prediction module; 2) the fitting module for the relationship between effect and pause rate; 3) the measurement module with correction terms. Extensive experiments were conducted on the real dataset of the Fujian Expressway, and the results show that the proposed method can be applied to measure the effect caused by service areas in the absence of service area entry data. The model can also provide references for other traffic indicator measurements under the effect of the service area.