Scientific and effective evaluation of civil aviation service quality is of great significance to improve customer satisfaction and the main competitiveness of civil aviation enterprises. In combination with the core ideas of the service quality model, this paper compares and analyzes the service quality evaluation process of airports and airlines from the two dimensions of service contents and evaluation indexes on the basis of literature arrangement and summary. Based on the SERVQUAL model and the "China Civil Airport Service Quality Evaluation Index System", the related contents of the system is appropriately revised combined with the characteristics of airport and airline services. To this end, the service quality evaluation indexes of airports and airlines are respectively built. The research shows that there are indeed some differences in five dimensions of evaluation indexes between airports focusing on ground services and airlines responsible for in-flight services. Only when scientific and reasonable evaluation index system for the quality of civil aviation transportation services is established for evaluation in line with the characteristics of civil aviation transportation services in the two scenarios, can the overall service level of passenger transportation in civil aviation industry be upgraded to achieve the high-quality development of civil aviation transportation industry in China.