Anti-acidification microbial consortium (AAMC) is effective in overcoming inhibition of microbial activity by acidification of composting material and avoiding the collapse of food waste composting under the synergistic action of acid-tolerant and acidophilic microorganisms. The degradation of organic substances could be accelerated by inoculation with AAMC. Complete degradation of organic matter and carbon refixation (the formation of humic substances) occur simultaneously during composting. Organic matter degradation has an interactive relationship with the formation of humic substances. The former provides raw materials for the latter. In order to explore the effect of inoculating anti-acidification microbial consortium (AAMC) on the quality of humic substances of food waste compost, the humic substances were grouped by resin column method and the influence of inoculating AAMC on molecular structure complexity and stability of the three fractions, such as fulvic acid, hydrophilic fraction and humic acid. In this study, Inoculation group (AAMC, Inoculation), alkaline compound treatment group (MgO and K2HPO4, AC) and natural composting group (C) were set. Three-dimensional fluorescence technology (EEM) was used to realize accurate and complete quantitative characterization of spectral properties of three humic fractions combined with two quantitative characterization methods FRI and PARAFAC. FRI results showed that the Pi, n values of those regions, which represented simple molecular structure components, such as carboxyl and protein source structure decreased in all three humic fractions after composting. The degree of reduction in the inoculation group was significantly greater than that in the control group and degree of reduction was in the order Inoculation>AC>C. The Pi, n values of those regions, which represented humic acid-like compounds with high aromaticity and polycondensation degree increased in all three humic fractions. The degree of increase in the inoculation group was significantly greater than that in the other two treatments and it was also in the order Inoculation>AC>C. PARAFAC results showed that the fulvic and humic acid fractions could be divided into short-wavelength, long-wavelength humic acids and protein-like substances such as tryptophan. The hydrophilic fraction could be further divided into short-wavelength humic acid, tryptophan and tyrosine components. At the end of composting, the Fmax of those components which were attributable to short-wavelength and long-wavelength humic acids increased, while the Fmax of those components which were attributable to protein-like substances such as tryptophan decreased. The increased (decreased) levels were the highest in the inoculation group and they were markedly higher in the inoculation group than those in AC and C groups. In summary, the results exhibited that inoculating of AAMC could significantly promote the complexity and stabilization of molecular structure, improve the aromaticity and polycondensation degree of humic fractions and the quality of humic substances in food waste compost, and facilitate conservation of water and fertilizer after compost was applied to the soil. AAMC has high ability of degrading and transforming small molecular organic acids, which could overcome low humification efficiency problem caused by the inhibition of acid accumulation on composting microbial activity. These might be closely related to high humification degree of inoculation group. Alkaline materials as additives could also promote the stabilization and structural complexity of humic fractions and increase the humification degree of compost to a certain extent. This may be related to the pH improvement of composting material, which enables the continuous degradation and transformation of small molecular organic acids and facilitates the humification process of compost.