<p>Humic acid (HA), a key component of soil humic substances, plays a crucial role in soil fertility and ecological functioning. To investigate HA structural heterogeneity under contrasting organic inputs, a soil incubation experiment was conducted with straw and biochar applied individually and in combination. HA was characterized using complementary techniques, including elemental analysis, electron paramagnetic resonance (EPR), 3D excitation-emission matrix fluorescence spectroscopy (3D-EEM), transmission electron microscopy (TEM), solid-state ¹³C nuclear magnetic resonance (¹³C-NMR), and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Biochar application preferentially enriched aromatic and structurally condensed components of HA, whereas straw inputs increased the abundance of oxygenated moieties associated with molecular biodegradability. Strikingly, their combined application enhanced HA radical concentration and chemical activity while favoring a shift in aromatic composition toward less highly condensed aromatic structures, resulting in HA molecular assemblages that combine features commonly associated with higher chemical reactivity and increased structural persistence. These findings suggest that soil HA formation under co-application is characterized by a reactivity-stability coupling, whereby labile, oxygen rich components are reorganized within aromatic and structurally persistent molecular frameworks, as revealed by complementary spectroscopic and molecular network analyses. This study provides new strategies and theoretical foundations for optimizing soil organic matter stability and fertility.</p> Graphical Abstract <p></p>