<p>Intercropping is widely practiced to improve crop yield and resources use efficiency. However, its effect on rice, especially the subspecies rice such as Indica and Japonica intercropping is elusive. A two-year field experiment (2021–2022) was conducted to assess the effects of Indica-Japonica intercropping on rice growth, yield, and quality. Results showed that intercropping increased the leaf area and efficient leaf area of Indica by 45% and 13.5%, and Japonica by 46% and 19% as compared to monocropping. At the system level, Indica-Japonica intercropping improved the yield indices including the number of effective panicles and panicles, spikelet fertility, and 1000-grain weight, leading to higher crop yield (18.5% and 39.5%) and biomass dry matter (51% and 20%) compared to Indica or Japonica under monocropping. The improved photosynthetic rate due to better light environments also contributed to higher intercropping crop yield. Though intercropping reduced the brown rice quality and chalkiness, but improved head mild rice rate. The higher LER (1.25), LEC (0.36), SPI (13.2), ATER (1.22), and LUC (186.86) values confirmed higher productivity and efficient land use under intercropping. The crowding index (K = 3.71) favoured intercropping, with Indica (aggressivity A_IR = 3.55) dominant over Japonica (aggressivity A_JR = -3.55). The competitive ratio (CR &gt; 0) indicated minimal competition for resources. This indicates that Indica-Japonica intercropping could improve the growth, yield and quality of rice by efficiently utilizing resources, thus offer a more sustainable rice production system compared to monocropping.</p>