The study entailed the continuous monitoring of rice-crab ecological farming systems over a span of 16 years to scrutinize the influence of distinct cultivation methodologies on the fundamental physicochemical attributes of paddy soils and the economic advantages of the ecosystem. The treatments encompassed the rice-crab farming system (CR) and the conventional single-crop paddy field (FP). The findings underscored that, relative to the conventional single-crop rice farming system, the rice-crab ecological farming system markedly ameliorated the physicochemical attributes of the soil, particularly within the initial 3 to 4 years, with comparatively negligible alterations in the subsequent 13 years, eventually attaining a relatively stable state. In synopsis, the soil bulk density witnessed a reduction of 0.05 g·cm^-3, while soil porosity exhibited an augmentation of 2.1%. The content of soil organic matter escalated from 25.5 g·kg^-1 to 28.4 g·kg^-1, reflecting an increase of 2.90 g·kg^-1. Additionally, the soil’s total nitrogen content experienced a rise of 0.19 g·kg^-1, whereas the levels of available nitrogen, phosphorus, and potassium surged by 21.2 mg·kg^-1, 2.23 mg·kg^-1, and 29.0 mg·kg^-1, respectively. With regard to nitrogen fertilizer utilization, the CR treatment demonstrated a notable enhancement of 10.3% over the FP treatment. Concerning the economic benefits derived from rice and crabs, no significant discrepancy was observed in rice yield. Nonetheless, the enhanced quality of rice precipitated a 13.8% escalation in rice prices. Furthermore, the crab production within the CR treatment yielded a net economic advantage of approximately 18,269 RMB per hectare, thereby accomplishing the objective of dual benefits stemming from rice and crabs.