In China, disordered development and utilization of land space usually lead to serious conflicts between urban, agricultural, and ecological spaces. The identification of these conflicts is an important basis for scientific zoning of the three types of spaces and has important theoretical and practical significance for the sustainable use of land space. In this study, a conflict identification method based on the space conversion matrix is proposed to provide a reference for scientific zoning of urban, agricultural, and ecological spaces. The method constructs several land space change indices, including overall conflict degree, type stability degree, and type conflict degree, to evaluate and identify the overall conflict degree, main functions, and main conflict types of evaluation units, respectively. This study used Hubei Province in China as an example to verify the method. Results showed that the main types of land space conflicts in Hubei Province in 2010–2016 were the occupations of agricultural space by urban space and ecological space by agricultural space. Moreover, high conflict areas were mainly concentrated in the central and eastern plains, especially the urban areas of prefectural-level cities. By comparing data between 2010–2013 and 2013–2016, the two major conflict types showed weakening and fragmenting trends. The land space conflict identification method proposed in this study demonstrates several advantages over previous methods. These advantages include the ability to evaluate conflict degree and identify conflict types simultaneously, the low requirement of data condition, and simple and intuitive representation of identification results.