The DEA model is used to analyze and evaluate the logistics efficiency of China’s nine coastal provinces from 2012 to 2016 by selecting the number of people employed in the transportation industry, the fixed asset investment in the logistics industry and the graded mileage as input indicators, and the added value of the logistics industry, the turnover of freight volume and regional GDP as output indicators. The results show that the DEA of logistics efficiency is effective in Zhejiang Province, Hebei Province, Jiangsu Province and Liaoning Province, but not in Guangdong Province, Fujian Province, Guangxi Zhuang Autonomous Region, Hainan Province and Shandong Province. The analysis results of the factors that affect the logistics efficiency of the nine coastal provinces show that the degree of influence of each index is different. The transportation, warehousing, postal workers and graded mileage in the input index have a great influence on the logistics efficiency of the nine coastal provinces, with the degree of influence being 0.031. The freight turnover in the output index has a great influence on the logistics efficiency in the nine coastal provinces, and the influence degree is 0.133. Therefore, it is suggested that provinces with effective logistics DEA should continue to maintain their own advantages and play a leading role in developing logistics in urban agglomerations and establishing a sound modern logistics management system. The provinces with non-effective logistics DEA should learn from the successful experience of other provinces and make corresponding adjustments according to their own actual conditions.