To address the challenges of exacerbated soil acidification and difficulty in achieving both fertilizer reduction and efficiency enhancement in southern China’s paddy soils, primarily caused by excessive chemical nitrogen fertilizer application, this study investigated the synergistic improvement effects of combining nitrogen reduction with a humic acid soil conditioner. A two-year field experiment (2023—2024) was conducted using plot trials in Jinyun County, Lishui City, Zhejiang Province. Three treatments were established: conventional fertilization (CK), 15% nitrogen reduction (85%N), and 15% nitrogen reduction combined with humic acid amendment (85%N+HA). Soil physicochemical properties, biological characteristics, and rice yield components were systematically analyzed. The results showed that compared with CK, 85%N did not significantly ameliorate soil acidity, whereas 85%N+HA significantly increased soil pH by 0.17 units and reduced the contents of exchangeable H⁺ and Al³⁺. Under nitrogen reduction, 85%N+HA effectively maintained the level of alkaline-hydrolyzable nitrogen and significantly enhanced the contents of available phosphorus and available potassium. Furthermore, this treatment significantly increased soil organic matter, promoted the formation of macro-aggregates, enhanced the activities of sucrase, urease, and acid phosphatase, improved soil bacterial diversity (Shannon and ACE indices), and significantly increased the relative abundance of Pseudomonadota. Ultimately, 85%N+HA significantly increased rice yield by 18.5% compared to CK, achieved through higher panicle number and more grains per panicle. In conclusion, the combined application of reduced nitrogen and humic acid amendment, through the synergy of chemical and biological processes, successfully mitigates soil acidification, enhances soil fertility, and increases rice yield while reducing nitrogen input, providing an effective technical pathway for the remediation of acidified paddy fields in southern China.