[Background] Configuring different types of measures reasonably in space to produce the comprehensive benefits in ecological, economic and social aspect under limited investment of soil and water conservation has become a hot research. Furthermore, solving the multi-objective optimal problem is the key because the optimal allocation of soil and water conservation measures in space refers to multi- objective. [Methods] This research focused on the area of Chanting County, Fujian Province of which soil is being serious eroded. The soil and water loss area in 2012 was as evaluation object of suitability of soil and water conservation measures. The study area was divided into the area of ecological natural restoration and artificial auxiliary control based on the suitability assessment of the enclosing measures. This paper constructed an optimal allocation model of water and soil conservation measures in space with the aim of minimum investment, maximum ecological benefits and maximum suitability in the artificial auxiliary management area, and adopted a fast and elitist multi-objective genetic algorithm (NSGA-II) to solve the model in order to screen out the best program. Moreover, the experimental results were verified and analyzed by using the reality of soil and water erosion control between 2013 and 2015. [Results] According to the optimized allocation results, the spatial distribution of soil and water conservation measures was directed by the maximization of ecological benefits and the maximization of suitability of spatial distribution in the case of stationary government investment funds. Calculating the investment cost, ecological benefits and suitability of optimization allocation layout and actual spatial layout of soil and water conservation measures, the results were as follow: the investment cost of actual layout was 6.964 5 *10⁷, the ecological benefits of actual layout was 7.908 0 *10³, and the suitability of actual layout was 1.953 3 *10⁴. However, the investment cost of optimized allocation layout was 6.579 1 *10⁷, the ecological benefits of optimized allocation layout was 7.907 3 *10³, and the suitability of optimized allocation was 2.054 1 *10⁴. It was found that the optimal allocation layout was significantly improved in terms of investment cost and suitability compared to the actual space layout of soil and water conservation measures. The reason that the ecological benefits were reduced was that the decrease of the invested cost inevitably led to the reduction of the ecological benefits. Moreover, the spatial distribution of soil and water conservation measures between optimal allocation and actual space layout was similar in most of regions, and the degree of similarity was 73.62%. [Conclusions] With the increase of evolution generation, the effect of optimal allocation of soil and water conservation based on NSGA-II algorithm was obvious, and the optimal allocation layout was reasonable and practicable, which can offer the decision- making basis for government implementing soil and water conservation measures.