Urea supplements, such as humic acids, could enhance fertilizer nitrogen use effectiveness. Melting is superior to mixing for humate urea application; however, the effects of diverse humate ureas from various coal sources on soil N supply remain unclear. This study compared the properties of two humic acids from different coal sources (HA1, weathered coal; HA2, lignite coal), and their impact on soil mineral N supply and the nitrate–ammonium ratio under flooded and 60% water-filled pore space (WFPS) over a 14-day incubation. Humate ureas stimulated soil mineral N accumulation and balanced the soil nitrate–ammonium ratio at 1:1; however, no significant difference existed between the two humate ureas under 60% WFPS. Humate urea enhanced soil ammonium nitrogen (NH₄⁺-N) retention and delayed nitrate nitrogen (NH₄⁻-N) release, leading to soil mineral N retention, especially in lignite humic acid urea (H2AU) treatments from lignite under flooding. Structural equation modeling (SEM) and linear regression revealed that humic acids elevated soil redox potential (Eh) and electrical conductivity (EC), stimulating soil N mineralization and adjusting the optimal nitrate–ammonium ratio. Humate urea improved soil mineral N supply compared to traditional urea treatments, and humic acids from lignite were more beneficial for crop cultivation from a mineral soil N supply perspective. These findings enhance our understanding of humate urea benefits and aid in optimizing humic acids application for N management.