Returning straw and green manure to the field is a vital agronomic practice for improving crop yields and ensuring food security. However, the existing research primarily focuses on drylands and low-fertility paddy fields. A systematic discussion of the yield-increasing mechanisms and soil response patterns of medium- and long-term organic fertilization in subtropical, high-organic-matter paddy fields is lacking. This study conducted a six-year field experiment (2019-2024) in a typical high-fertility rice production area, where the initial organic matter content of the 0-20 cm topsoil layer was 44.56 g kg. Four treatments were established: PK (no nitrogen, only phosphorus and potassium fertilizer), NPK (conventional nitrogen, phosphorus, and potassium fertilizer), NPKM (NPK + full-amount winter milk vetch return), and NPKS (NPK + full-amount rice straw return). We collected 0-20 cm topsoil samples during key rice growth stages to monitor the dynamic changes in nitrate and ammonium nitrogen. The rice SPAD, LAI, plant height, and tiller number were also measured during the growth period. After the six-year rice harvest, we determined the properties of the topsoil, including its organic matter, pH, total nitrogen, phosphorus, potassium, available phosphorus and potassium, and alkali hydrolyzable nitrogen. The results showed that, compared to NPK, the organic matter content of the topsoil (0-20 cm) increased by 6.36% and 5.16% (annual average increase of 1.06% and 0.86%, lower than in low-fertility areas) in the NPKS and NPKM treatments, respectively; the total nitrogen, phosphorus, and potassium content increased by 16.59%, 8.81%, and 10.37% (NPKS) and 6.70%, 5.12%, and 11.62% (NPKM), respectively; the available phosphorus content increased by 21.87% and 8.42%, respectively; the available potassium content increased by 47.38% and 11.56%, respectively; and the alkali hydrolyzable nitrogen content increased by 3.24% and 2.34%, respectively. However, the pH decreased by 0.07 in the NPKS treatment while it increased by 0.17 in the NPKM treatment, respectively, compared to the PK treatment. NPKS and NPKM improved key rice growth indicators such as the SPAD, LAI, plant height, and tillering. In particular, the tillering of the NPKS treatment showed a sustained advantage at maturity, increasing by up to 13.64% compared to NPK, which also led to an increase in the effective panicle number. Compared to NPK, NPKS and NPKM increased the average yield by 9.52% and 8.83% over the six years, respectively, with NPKM having the highest yield in the first three years (2019-2021) and NPKS having the highest yield from the fourth year (2022-2024) onwards. These results confirm that inputting organic materials such as straw and green manure can improve soil fertility and rice productivity, even in rice systems with high organic matter levels. Future research should prioritize the long-term monitoring of carbon and nitrogen cycle dynamics and greenhouse gas emissions to comprehensively assess these practices' sustainability.