Health evaluation of land use system is a significant foundation for improving the health of land use system and the sustainable land use of land. In view of the health on land use system's uncertainty, the authors constructed an evaluation index system based on the PSR(pressure-state-response) model, and established the health evaluation model on land use system based on the set pair analysis and the improved entropy method, and utilizing set pair analysis theory and the malleability of the original relation degree to extend the comprehensive evaluation ranking from 3 levels to 5 levels, and then conducted an evaluation of the health on land use system of China. The results showed:(1) The health of land use system in China was gradually improved from unhealthy to critical state from 1999 to 2008, but the level of "critical state" was not high in 2008;(2) Crucial constraint factors for improving land use system health include the growth rate of fixed asset investment, per capita arable land, land reclamation rate, extent of soil erosion and per capita GDP. The evaluation index system based on the PSR model can accurately reflect the relationship between various elements of the land use system health, while the set pair analysis can discover specific problems in land use system. Therefore, the evaluation index system and the set pair analysis are suitable to assess the health of land use system.