This paper put forward the composite index method to calculate the lowest ecological water level and select 3index, that is natural water level date, the lake morphology, reed to calculate the lowest ecological level according to the circs of Lake Bosten. The result are 1047.06m, 1047.41m, 1047.20m, respectively. According to every factor contribution to the lowest ecological level, the weighting coefficient of every factor was considered. The final result show that the only when the water level is high than 1047.16m can the ecosystem structure be guaranteed, and the normal ecosytem function be fully played, the bio-diversity and the ecosystem integrity be maintained. Therefore, it is reasonable that the 1047.16m as the lowest ecological water level.