Gluten-free rice bread made from japonica rice finds challenge in achieving a good shape and structure, presenting a significant obstacle in the baking industry. This study aims to improve the quality of rice bread with japonica rice flour by hot extrusion treatment (without additives). The effects of extrusion on the amylose content, gelatinization degree, hydration capacity, short-range molecular ordering, and microstructure of japonica rice flour were investigated. The results show that the amylose content of the extruded flour increased by 12.43% and the gelatinization degree of it increased by 13.23 times, showing disrupted starch granules, numerous pores, and a better hydration capacity. The addition of extruded flour improved the overall viscoelasticity of the batter. Compared to the control group, the specific volume and porosity of the optimized rice bread were increased by 19.46% and 61.92%, respectively. The gas cell density was increased by 4.63 times, and the average gas cell area of rice bread was reduced by 47.14%. The correlations among the raw material properties of rice flour, the batter properties, and the quality of rice bread products were revealed by principal component analysis. This study demonstrates that the addition of moderate amounts of extruded japonica rice flour could improve the quality of rice bread products.