With the rapid development of industrialization in China, the demand for transportation service has increased substantially, causing huge energy consumption in transport sector. The land transportation (including railway transportation and highway transportation) is the most important source of energy consumption in China. In this study, the parallel Slack-Based Measure (SBM) model and three-stage of Data Envelopment Analysis (DEA) approach are combined to measure the energy efficiency of land transportation system and two subsystems from 2013 to 2017 with excluding the non-management factors. The empirical results lead to four conclusions: (a) non-management factors do exert unfavorable influence on the energy efficiency measurement, ignoring which will overestimate the efficiency value. (b) There exist significant area disparities in energy efficiencies of the land transportation and its two subsystems. (c) The energy efficiencies of the whole land transportation and the highway transportation present a significant upward trend, while the changing trend is not promising for the railway transportation. (d) The railway transportation has a greater impact on the efficiency of the whole system in 2013 and 2014, which has weakened in the next three years.