A model for prediction of a basin’s ecological health was established through the coupling of three methods, including the pressure-state-response(PSR)model, the analytic network process(ANP)model, and the cellular automaton-Markov(CA-Markov)model. Based on data from the years 1990, 2000, 2010, and 2020, the matter element analysis method, the TOPSIS method, and the fuzzy comprehensive evaluation method were used to analyze the ecological health of the Xinjiang Basin. The results show that, from 1990 to 2000, the ecological health status of the Xinjiang Basin was at the grade I level, which was a very healthy status, and from 2001 to 2010, the basin’s ecological health status continuously deteriorated, reaching the grade V level, which was an unhealthy status. The prediction results show that, in the 2020s, the ecological health status of the Xinjiang Basin will improve, reaching the grade III level, which is a sub-healthy status. Although the status will have improved, it is necessary to pay a high degree of attention to the management and maintenance of the basin’s ecological health.