The effect of bacteria content in wheat flour on shelf life and storage stability of fresh wet noodles (FWNs) was evaluated in this study. Nine kinds of wheat flour with different bacterial contents were selected to make FWNs. With the increase in total plate count (TPC) from 120 CFU/g to 5500 CFU/g in flour, the shelf life of FWNs decreased from 23 d to 9 d at 4 °C. During storage, the acidity increased, which was significantly correlated with the change of TPC (p < 0.05), and the pH value and L* value of FWNs decreased significantly (p < 0.05). Changes in viscosity characteristics of starch components were also detected, the higher the TPC in flour, the more obvious the viscosity decreased. Moreover, sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) showed that with the deterioration of FWNs, some low molecular weight protein subunits increased; texture analysis showed that the hardness of noodles increased firstly and then decreased, the adhesiveness increased and the springiness decreased during storage. In summary, choosing flour with low TPC to prepare FWNs can extend the shelf life and slow down the quality deterioration of FWNs during storage at 4 °C.