Soft wheat flour doughs were prepared with different levels of salt (NaCl) or baking soda (NaHCO). Oscillation rheology, elongational viscosity, and extensibility of doughs were tested to evaluate the effect of salt and baking soda on the physical properties of doughs. Furthermore, a series of physical-biochemical analytical techniques were used to investigate gluten polymerization in doughs, including zeta potential analyzer, Fourier transform infrared spectroscopy (FTIR), spectrophotometer, and reversed-phase high-performance liquid chromatography (RP-HPLC). The addition of high levels of NaHCO (1.0% fwb), either by itself or in combination with NaCl, increased dough strength, elongational viscosity, and viscoelasticity. RP-HPLC results demonstrated macromolecular aggregation of gluten proteins in the presence of NaCl or NaHCO. The addition of NaHCO or NaCl also decreased both free sulfhydryl content and random-coil structure of gluten isolated from the doughs. Overall, NaCl and NaHCO induced the changes of molecular conformation of gluten, which impacted the physicochemical qualities of soft wheat flour dough. This study provides a better understanding of salt and baking soda functionality in the formation of soft flour dough, which will support the searching of feasible sodium reduction strategies in soft flour bakery products.