Different amounts of wheat straws were incorporated into the two paddy soils (silty soil and clayed soil) to explore the impacts of straw return on the diversity and composition of fungal community after 30 days of flooding incubation based on conventional analysis and high-throughput sequencing. Results showed that straw addition significantly decreased the diversity of fungal community in the silty soil but not in the clayed soil. Compared to un-amended soils, straw addition changed fungal community composition in the silty soil, but no significant difference was found in fungal community compositions between different rates of straw amendment. Unlike to the silty soil, for the clayed soil, significant differences were found in soil fungal community compositions between un-amended soils and high rates of straw concentrations (50 g/kg), while no significant difference between un-amended soils and soils amended with low rates of straw concentrations (10 and 20 g/kg). pH, EC and SOM were identified by CCA analysis as variables that significantly contributed to the variance of fungal community in the silty soil, while pH, EC, SOM and C/N ratio as variables in the clayed soil. In conclusion, straw addition significantly changed fungal community composition by altering soil properties, and the response of soil fungal community composition to straw return depended on soil type.