Soil salinity represents a significant factor affecting agricultural productivity and crop quality. The present study was conducted to investigate the effects of soil conditioner (SC) comprising halotolerant microorganisms on the soil fertility, yield, rice quality, and the physicochemical and structural properties of starch in hybrid rice under saline conditions. The experimental treatments were composed of two high-quality hybrid rice varieties, i.e., ‘Y Liangyou 957’ (YLY957) and Jing Liangyou 534 (JLY534), and two soil amendment treatments, i.e., the application of SC at control levels and 2250 kg hm−2, or ‘CK and SC’, respectively. The crop was subjected to a mixture of fresh and sea water (EC 11 dS/m). The results demonstrated that the application of SC significantly enhanced the rice yield under salt stress conditions owing to an increase in the number of grains per panicle. Furthermore, SC was found to be effective in improving the organic matter and soil nutrient content. Furthermore, the application of SC resulted in an improvement in antioxidant defense, higher leaf SPAD values, and greater crop biomass, as well as the translocation of photo-assimilates at the heading stage. The application of SC not only improved the milling and appearance quality but also enhanced the taste value of rice by increasing the amylose and reducing the protein content. Furthermore, the application of SC also decreased the indentations on the surfaces of starch granules and cracks on the edges of the granules. The rice varieties subjected to SC exhibited excellent pasting properties, characterized by reduced proportions of amylopectin short chains and a lower gelatinization temperature and enthalpy of gelatinization. Overall, these findings serve to reinforce the efficacy of soil conditioner as a valuable tool to improve rice productivity and sustainability with improved rice grain quality under saline conditions.