The results of model simulation of the humus state of arable soils in the Western Siberia based on long-term stationary studies and agrochemical monitoring of agricultural lands are presented. The following were studied: leached chernozem; podzolized chernozem; meadow-chernozem and dark gray forest soils. It was found that the nature of the root system formation depends on the biological characteristics of crops and cultivation conditions (the level of mineral nutrition, moisture). The mass of crop-root residues, as well as straw, is in close correlation with the yield of grain crops. Based on the actual data, regression equations were obtained with a high degree of reliability of the calculated data (approximation coefficient from R2= 0.84 to R2 = 0.93). Using the balance model of humus formation, it was found that the podzolized chernozem and dark gray forest soil were the least resistant to the anthropogenic factor. As a result of prolonged agricultural activity (52 years), humus losses in them amounted to 28 and 37 t/ha, which corresponded to annual losses of 0.54 and 0.71 t/ha. Leached arable chernozems lost 24 t/ha of humus, which corresponded to annual losses of 0.46 t/ha. In the course of the study, it was revealed that the arable land of the Western Siberia has a stable negative balance of humus state, which requires optimization of the farming system in the region.