Secondary salinization induced by brackish water irrigation has forced agricultural development to increasingly rely on soil management. A two-year field experiment was conducted to explore the effects of different straw incorporation rates (SIRs) within 0 to 20 cm topsoil on the soil water–salt balance, maize yield production, and water use efficiency (WUE) under brackish water irrigation in a naturally non-saline area. Air-dried wheat straw was applied at the rates of 0, 4.5, 9.0, 13.5, and 18.0 t ha−1 (R0–R4) and two salinity levels of irrigation water with the salt content of 1.92 dS m−1 (SL) and 3.20 dS m−1 (SH) were applied for simulating the scenarios of secondary salinization. Results demonstrated that straw incorporation markedly increased the soil water content during two growing seasons, and SIR was directly correlated to the deep percolation, but inversely correlated to the soil water depletion, under both the SL and SH condition. Meanwhile, straw incorporation led to the increase in salt content within the straw incorporation zone, but the total mass of salt deposited in the 0–100 cm soil profile was comparatively reduced as SIR increased due to the increased deep percolation for salt leaching, and such relative alleviation was more pronounced under the SH condition. The significantly increased maize yield and its corresponding WUE were obtained in treatments with high SIR levels. Additionally, an exponential function was used to describe the trend of the yield-increasing rate as SIR increased, and the theoretical maximum of grain and biomass yield calculated from the fitting results were 6483 in 17,282 kg ha−1 under SL, and 5440 and 14,501 kg ha−1 under SH, respectively. Results in this study would be helpful in the adoption of straw incorporation and brackish water irrigation in ways that facilitate soil water availability and reduce the risk of soil salinization.