Fermentation plays a crucial role in traditional Chinese mianpi processing, where short-term natural fermentation (within 24 h) is considered advantageous for mianpi production. However, the influence of short-term natural fermentation on the properties of wheat starch is not explored yet. Hence, structural characteristics and paste properties of wheat starch during natural fermentation were investigated in this study. The findings revealed that fermenting for 24 h had a slight effect on the morphology of wheat starch but significantly decreased the particle size of starch. Compared to native wheat starch, the enzyme activity produced during fermentation may destroy the integrity of starch granules, resulting in a lower molecular weight but higher relative crystallinity and orderliness of starch. After 24 h of natural fermentation, higher solubility and swelling power were obtained compared to non-fermentation. Regarding paste properties, fermented starches exhibited higher peak viscosity and breakdown, along with lower final viscosity, tough viscosity, and setback. Furthermore, the hardness, gel strength, G', and G" decreased after fermentation. Clarifying changes in starch during the short-term natural fermentation process could provide theoretical guidance for improving the quality and production of short-term naturally fermented foods such as mianpi, as discussed in this study.