Social and economic development, production and living needs, other human behavior requirements and various ecological engineering construction are considered as the main influencing factors of land spatial pattern changes and land ecological security risks in rocky desertification areas. From the perspective of land-use spatial change, the impact of human activities and resource utilization on land ecological security risks can be more intuitively analyzed. Based on the land-use change survey data of Phase 4 of Honghe Prefecture, China, the study measures the characteristics of land-use transfer flow and land-use dynamic change, analyzes the main influencing factors and comprehensively constructs the land ecological security risk index model, on which the land ecological security risk is classified. The results showed that the land ecological security risk degree in the three stages of the study area from 2014 to 2020 was 2016–2018 > 2018–2020 > 2014–2016, and had obvious regional characteristics. Among many influencing factors, the different activities/projects (positive or negative) types, time and intensity affect the land-use transfer flow and dynamic change characteristics, resulting in corresponding changes in the risk of land-use ecological security. Among them, man-made destruction and construction activities have the most significant negative effects on land ecological status. The empirical analysis proved that building an ecological security risk index based on the direction, area, and rate of spatial changes in land-use can accurately reflect the degree of desertification risk in rocky desertification areas. The study results can provide important information on the impact of regional development and the environmental governance policies of the land-use change in rocky desertification areas.