Human societies are essentially composed of three different systems:social, economic, and natural. Studies on the ecological niche of social, economic, and natural complex ecosystems has significant importance on the activities and lives of humans in a complex ecosystem and the sustainable development of land. In this study, a set of indicator systems were established to evaluate the ecological niche of a complex ecosystem in Sichuan Province from 2001 to 2010, based on the evaluation index theory of sustainable development, urban livability, and human development. The integrated ecological niche of the complex ecosystem included four sub-niches:natural resources, environment, economy, and society. These sub-niches comprised many single-item indicators. A coupling projection pursuit model, in which a parallel-simulated annealing algorithm was employed in parameters of optimization, was applied to quantitatively analyze and assess the ecological niche of the complex ecosystem and each sub-niche. Our results indicate that the ecological niche of the complex ecosystem in Sichuan Province first decreased from 3.1325 in 2001, to 2.8499 in 2005, and then increased to 3.3304 by 2010. Our results indicate that, as public awareness of environmental protection increases, the regional ecological niche index also increases. Additionally, the ecological and environmental situation has improved. The correlation coefficient between the economic niche system and the social niche system was 0.9957, indicating that the two sub-niches develop in synchrony. In contrast, the correlation coefficient between the economic niche system and the environment niche system was -0.9346, suggesting an obvious negative correlation. In total, the resource sub-niche system displayed an upward trend. The best projection direction value reflects the impact of each regional ecological niche evaluation index in the projection pursuit model. The large index value of the ecological niche evaluation corresponds with a great impact on the ecological niche. Four indicators of the environmental-ecological sub-niche have significant impacts on the regional ecological niche. This can further influence the weight of the regional ecological niche evaluation index based on the value of the best projection direction. The ten most influential regional ecological niche evaluation indicators are (from most influential to least influential):Industrial soot emissions > industrial dust emissions > industrial sulfur dioxide emissions > per capita energy yield > total industrial waste water emissions > non-agricultural population accounts for the proportion of the total population > rate of plant coverage in urban areas > per capita revenue > population density > drought affected areas. Of these, four indicators belong to the environmental-ecological niche sub-system, which shows that this system has an essential influence on the entire ecological niche of the area. In comparison, the traditional polygon synthesis index method was used to evaluate the ecological niche in Sichuan Province. The results are in agreement with those calculated by the current projection pursuit algorithm, which verified the correctness of our improved algorithm. Furthermore, the projection pursuit algorithm may be used to discover the rules among data through automatic exploration, and thus has excellent potential in data analysis and processing applications. This algorithm may be used to avoid the subjective one-sidedness of the traditional evaluation method of weight determination. The projection pursuit model, optimized by simulated annealing, is practical and feasible in composite niche evaluation. This model is able to provide an important basis for scientific decision making in regional ecological management.