Duckweed growing in paddy fields (DGP) has substantially increased because of the effects of climate warming and/or eutrophication in irrigated water. Previous studies have primarily focused on investigating the effects of DGP as a nonchemical agent for enhancing rice productivity on nitrogen utilization in rice paddy fields. However, how DGP impacts rice yield remains poorly understood. Therefore, a field experiment with three representative rice cultivars was conducted to determine the effects of DGP on rice yield, considering ecological factors, photosynthetic capacity, spectral changes, and plant growth. The results showed that DGP significantly reduced the pH value by 0.6 and the daily water temperature by 0.6 °C, accelerated rice heading by 1.6 days and increased the soil and plant analyzer development (SPAD) and photosynthetic rate of leaves by 10.8% and 14.4% on average, respectively. DGP also markedly enhanced the values of various vegetation indices such as RARSc, MTCI, GCI, NDVI705, CI, CIrededge, mND705, SR705, and GM, and the first derivative curve of the rice canopy reflectance spectrum exhibited a ‘red shift’ phenomenon upon DGP treatment. Changes in the aforementioned factors may lead to average increases of 4.7% in plant height, 15.0% in dry matter weight, 10.6% in panicles m−2, 2.3% in 1000-grain weight, and ultimately a 10.2% increase in grain yield. The correlation observed suggested that the DGP-induced enhancement in grain yield can be achieved by reducing the pH and temperature of the paddy water, thus enhancing the SPAD value and photosynthesis of leaves and stimulating rice plant growth. These results could offer valuable theoretical support for the future sustainable development of agriculture and the environment through the biological synergy between rice and duckweed.