[Objective] Two thermophilic fungal species which were isolated from the compost of cotton residue in Xinjiang were identified, and increased degradation rate of straw by optimizing the impact factors for cellulase production. [Methods] Two thermophilic fungal species were identified by morphological observation and analyzed the clone of the ITS gene fragment, The filter paper enzyme activity (FPA) of fungi was determined when they grown in a series of liquid state media containing pretreated natural cellulose as the carbon source, different nitrogen source, different initial pH, different inoculated amount and culture time, by analyzing the change of the FPA. [Results] Z1 is Aspergillus fumigatus Fresen and Z2 belongs to Myceliophthora Cost. (homology 97%). The filter paper enzyme activity (FPA) of fungi was determined when they grown in a series of liquid state media containing pretreated natural cellulose as the carbon source, different nitrogen source, different initial pH, different inocu-lated amount and culture time, by analyzing the change of the FPA, we had got the optimal conditions of fermentation. Under the optimal conditions, the decomposing (cotton residue) rate of Z1 was 10.19% and MS was 53.45% for 10 days, the decomposing (wheat straw) rate of Z2 was 27.50% for 10 days. [Conclusion] Degradation rate of straw MS better than single strains was more than half. It has great potential in recycling natural cellulose of Xinjiang when applied the fungal, which can degrade not only cotton residue but also wheat and rice straw, it has great potential for further apply in straw degradation.