The paper studies the processes of transformation of the molecular structure of humic (HA) and fulvic acids (FA) of leached chernozem under the influence of fertilizers and meliorant. The research was carried out under the conditions of many years of stationary experiment of the Department of Agrochemistry, Soil Science and Agroecology of the FSBEI HE Voronezh SAU. Samples of leached low-humus thin heavy-loamy chernozem were analyzed. The isolated and purified preparations of HA and FA were studied on a SM2203 spectrofluorimeter in the ultraviolet and visible ranges. The paper also presents the results of determining the most important physical and chemical properties of soil variants using various fertilizer and meliorant systems. Limed variants have optimal indicators. Based on the analysis, it can be assumed that the FA molecules of the variant with a double dose of mineral fertilizers on the background of manure differ in a developed aliphatic part, have many auxochromic substituents. HA of the same variant are characterized by a high condensation of nuclear structures. The HA and FA molecules of the variant with the joint application of fertilizers and meliorant have a more complex structure of the nuclear and peripheral parts. According to the results of calculations of extinction coefficients, it was found that liming contributes to the accumulation of more mature forms of humic acids.