Application of thermophilic composting (TC) is limited due to poor efficiency and long composting period. Hyperthermophilic composting (HTC) could effectively overcome this defect. Here, the transformation of humic acid (HA) in both HTC and TC was characterized and compared to investigate the roles of HTC toward accelerating the formation of HA. In HTC, the highest temperature was 96.6 °C, and the hyperthermophilic and thermophilic phases exceed 18 days. The degree of polymerization (DP) in HTC increased to 1.27 on day 27, while it only increased to 1.15 at the end of TC. The elemental composition of the HA in HTC showed higher O atomic content (36.3%) and lower C/N atomic ratio (6.5) compared with TC. These changes indicated that HTC could significantly accelerate oxidized and polycondensed reactions for HA formation, which resulted in the shortening of composting period to 27 days. The maximum fluorescence intensity (Fmax) of humic-like components were achieved faster in HTC (Fmax = 1649.9) than in TC (Fmax = 1316.9), implying that HTC promoted the polycondensation of small molecular components to form HA with larger molecular weight and higher degree of aromatization. Two-dimensional FTIR correlation spectroscopy (2D-FTIR-COS) analysis demonstrated that HTC prevented the HA precursor from condensing before it was deeply oxidized, and increased the content of small molecules rich in carboxyl moieties. Based on the evolution of the molecular structure of HA, the level of oxidation of HA precursors was a key factor to determine the degree of polymerization and the degree of HA humification.