Humic acids (HAs) regulate soil chemical reactivity and improve many soil functions. The amendment of soil with organic materials increases soil organic matter (SOM) content and promotes the formation of HAs. However, the effect of the type, frequency and duration of amendment, and pedoclimatic conditions on SOM transformation and HA structural changes remains unclear. Herein, four experimental field sites (S1–4) with short-to-long-term organic fertilisation schemes were used to assess the effects of such factors, i.e., S1: loamy sand amended once with farmyard manure (FYM), brown coal waste (BCW), and biochar (BIO) for 0.5 and 1.5 years; S2: silt loam amended once with BIO for 8 years; S3: loamy sand amended every 5 years with FYM for 94 years; and S4: clayey silt amended every 2 years with FYM for 116 years. All HAs were extracted and analysed for structural differences by elemental analysis (EA), attenuated total reflectance–Fourier transform infrared spectroscopy (ATR-FTIR), solid-state cross polarisation magic angle spinning nuclear magnetic resonance spectroscopy (CP/MAS 13C-NMR), and differential scanning calorimetry (DSC). Results from EA, FTIR, and NMR showed that the long-term samples from S3 (treatments, T9–T10) and S4 (T11–T12) had the greatest aromatic characteristics, which increased with FYM amendment (T10 and T12). These agreed with DSC data, which indicated lower aliphatic contents compared with other samples. Samples from S2 (T7–T8), with receded amendment effects, had less aromatic and greater aliphatic characteristics compared with the short-term samples, S1 (T1–T6). In S1, structural changes were limited, but aromaticity increased with BIO (T3 and T6) compared with corresponding FYM (T1 and T4) and BCW (T2 and T5) amendments due to inherently high aromatic groups in the former. Overall, the results showed that the site (due to differences in pedoclimatic conditions), field age of OM, and amendment frequency were the main factors that influenced HA structure, and hence SOM transformation. Regular, long-term organic amendment increases the aromatic characteristics of HAs, which can improve soil functionality, but short-term structural improvements are achievable only when amending material is rich in aromatic compounds.