Land ecological security is the foundation of resources, environment and ecosystem health. Focusing on the incompatibility of various evaluation indexes of the land ecological security system, this paper evaluated land eco-security using the theory of matter element analysis. An evaluation index system of land ecological security was established based on EES-PSR model. The land ecological security classification standard, the evaluation index and its characteristic value were regarded as matter-elements. Through the normalization of the evaluation index and the actual data to be evaluated, a comprehensive evaluation model of land ecological security was established after getting the classical domain, joint domain, weight coefficient and correlation degree of the matter element model. The evaluation model was applied to the land ecological security assessment in Heilongjiang, Harbin. With the support of GIS technology, the visual expression and analysis of the evaluation and evaluation of land ecological security in the study area were achieved. The results showed that during 2011 to 2015, the level of land ecological security in Harbin changed from “insecurity” to “security”, and the most prominent change occurred after 2013. The area of afforestation, the proportion of primary industry to GDP, the consumption of million yuan GDP energy (standard coal), the rate of industrial waste water treatment and the area of public green space per capita had been “ insecurity” for many years and were the restriction factor of land ecological security level in Harbin City. In 2015, the level of land ecological security was low in the middle and southwest of Harbin, but it was higher in the northern and southeastern regions. It is concluded that matter element model analysis had certain guiding significance for regional land ecological security assessment.