The refined flour and whole grain flour of the same variety of wheat were used as raw materials to produce sourdough steamed bread by backslopping fermentation. The effects of white flour and whole grain flour on the microbiota of backslopping fermented sourdough and the physicochemical properties of steamed bread were investigated by comparing the differences between the sourdough microbiome and the properties of steamed bread. The results showed that the differences in fungal communities between mature refined flour and whole wheat sourdough were mainly reflected in the differences in fungal community structure. Blumeria graminis was the dominant fungus in refined flour sourdough, while Saccharomyces sp. was the dominant fungus in whole wheat sourdough. The physicochemical properties and sensory quality of steamed bread made from backslopping fermentation with whole wheat and refined flour were compared comprehensively. The results of principal component analysis showed that the preparation method was the main factor affecting the physicochemical properties of steamed bread, while the flour type (refined flour and whole wheat flour) was the secondary factor. Finally, Person correlation analysis proved that six key microorganisms had significant and specific effects on multiple physicochemical properties of refined flour and whole wheat steamed bread. In conclusion, the results proved that backslopping fermentation could effectively improve and enhance the comprehensive physicochemical properties of wheat steamed bread, and whole wheat flour could further improve the nutrition, function and sensory quality of wheat steamed bread compared with refined flour. These results provided theoretical insights and experimental basis for the development and application of whole wheat steamed bread.