Despite straw application within rice agriculture being widely practiced, both in China and globally, there remain few studies on the maize straw substituted for chemical fertilizers. In this study, maize straw substituted for chemical fertilizers to a double-cropping rice field and compared the effects of medium (MS 9,600 kg·ha−1·year−1) and high (HS 19,200 kg·ha−1·year−1) application on rice yield and soil characteristics with that of the application of single chemical fertilizers (CF) over a period of 1982 to present. The yields of late and early rice increased by 42.66 and 25.04% in 2019 and 2020, respectively. The soil bulk density of MS and HS decreased significantly by 15.94 and 33.35% compared with that of CF, whereas total soil porosity increased significantly by 9.46 and 20.17%, respectively. Long-term straw application significantly improved the soil stable aggregates content (> 0.25 mm). Straw application increased soil urease, protease, alkaline phosphatase (ALP), acid phosphatase (ACP) and catalase activities, microbial biomass carbon (C), microbial biomass nitrogen (N), and soil nutrients content compared with CF, especially HS. Correlation analysis showed that double-cropping rice yield was highly significantly correlated with soil bulk density, total porosity, catalase, microbial biomass C, microbial biomass N, and available P. In conclusion, maize straw substituted for chemical fertilizers not only makes rational use of straw resources, but also improves soil characteristics to improve crop yield.