Controlled-release urea (CRU) fertilizer application has been shown to improve crop yield and nitrogen (N) use efficiency. However, its effects when mixed with conventional urea fertilizer on soil aggregate stability, humic acid (HA) molecular composition and crop N uptake remain unclear. Soil and plant samples were collected from a long-term (2008–2019) experiment on field maize (Zea mays L., ‘Zhengdan 958’) which included two types of fertilizers [conventional urea fertilizer (CUF), blended CUF with CRU fertilizer (CRF)], four N application rates (0, 150, 300 and 450 kg ha⁻¹), each in three replicates. The results showed that at 300 kg N ha⁻¹, compared to CUF treatment, the CRF treatment significantly improved soil aggregate characteristics [aggregate content with particle size larger than 0.25 mm (R_0.25) by 9.6%, mean weight diameter by 19.8%, and geometric mean diameter by 21.7%]. CRF treatment also increased HA content by 5.5%, fulvic acid (FA) by 5.5%, lignin-like molecules by 0.94 times, and protein-like molecules by 3.69 times. At grain-filling stage, CRF treatments significantly increased the sum of soil NH₄⁺-N and NO₃⁻-N content by 23.3–24.5%, sap bleeding rate by 12.8–18.2% and N delivery rate through bleeding sap by 60.6–87.7% compared to CUF treatments at the same N application rate. At the same rate of N application, the CRF treatments significantly improved the average yield during three growing seasons by 9.4–14.0% in contrast with CUF treatments. The regression equations showed that the maximum yield was 8294 kg ha⁻¹ for CUF at the application rate of 312 kg N ha⁻¹ while it was 9890 kg ha⁻¹ for CRF at the application rate of 286 kg N ha⁻¹. We conclude that the long-term application of CRF changed the HA molecular structure, enhanced the water stable aggregates, improved crop N uptake, and increased economically viable maize yield.