The rapid development in economy and the change in land use structure can lead significant spatial differences in regional land use efficiencies. In this paper, Chongqing City was taken as the study area, the spatial differences and the influential factors in land use structure efficiencies from 2004 to 2013 were analyzed by using SBM-Undesirable model, Theil index and Moran’s I index. The results showed that: 1) Average efficiency of land use structure showed a trend of left-oblique "M", environmental negative output had a negative effect on land use structure efficiency, pure technical efficiency was the main cause for the change of technical efficiency; 2) Theil index showed an adverse trend as land use structure efficiency, obliquely upwards "W", its gradual increase indicated the enlarging spatial gap of land use structure efficiency, mainly due to the change in group gap. 3) Land use structure efficiency had spatial positive correlations with economic development, industrial structure, population urbanization and land urbanization, but spatial negative correlation with rural residential land, indicating the promotion of land urbanization on the internal optimization of urban and rural construction land structure.