Soil fertility is one of the most important influencing factors on the rice yield. Among them, the relationship between soil physical and chemical properties and rice yield can greatly contribute to rice production and fertilizer cultivation in different regions. This study aims to analyze the absolute rice yield, relative yield, and sustainable yield index on the county scale. The research area was also selected as Fangzheng County in northeast China, Ningxiang City in the middle reaches of the Yangtze River, and Jinxian County in the middle and lower reaches of the Yangtze River. The key factors of soil fertility were then determined to affect the rice yield in different regions. The results show that the two-season rice yield (9414.89 kg/hm²) in Ningxiang City was significantly higher than that in Fangzheng County (8224.31 kg/hm²) and Jinxian County (5691.38 kg/hm²) in the late season, due to different cropping patterns. But the average relative yield in Fangzheng County (89.88%) was significantly higher than that in Ningxiang City (73.84%) and Jinxian County (65.67%). The sustainable yield index of Fangzheng County was also higher (0.86), indicating high yield and stability. Furthermore, the low, medium, and high yield levels were calculated using relative yields. Therefore, the soil fertility index and integrated fertility index of Fangzheng County, Ningxiang City, and Jinxian County were higher under the high yield level. Among them, the soil organic matter index, available nitrogen index, and integrated fertility index of Fangzheng County at the high yield level increased by 25.50%, 31.17%, and 25.45%, respectively, compared with the low yield level. The soil available phosphorus increased by 35.41% in Ningxiang City, compared with the low yield level. The soil organic matter, available nitrogen, available phosphorus, available potassium, and integrated fertility index of Jinxian County showed that the high yield level was significantly higher than the middle and low yield levels, which increased 13.28%-27.28%, 21.45%-34.82%, 62.42%-111.90%, 29.51%-59.51%, and 34.21%-75.86%, respectively. There was no significant difference in the soil pH value among different yield levels. There was a variation in the fertility influencing factors on the relative yield in different counties. The soil's available phosphorus, nitrogen, and organic matter content were the key fertility factors for the sustainable yield index of rice in Fangzheng County, Ningxiang City, and Jinxian County, respectively. Some suggestions were provided for soil fertilizer cultivation in the high and stable rice yield at the county scale. In Fangzheng County, the soil available phosphorus shared the largest relative contribution to the rice sustainable yield index (8.68%), followed by organic matter and available potassium. In Ningxiang, the relative contribution of soil available nitrogen to rice sustainable yield index was 12.92%, followed by pH. In Jinxian County, the soil organic matter shared the greatest impact on the rice sustainable yield index (15.37%), followed by available nitrogen and available phosphorus. As such, there was the highest influencing level in the sustainable production of rice available phosphorus in the soil index, followed by available potassium and available nitrogen. Therefore, Fangzheng County should be focused on the soil available phosphorus in future rice production. While Ningxiang and Jinxian County should increase the soil available nitrogen and organic matter contents.