The basis of cultivated lands consists of the interacting populations of annual and perennial weeds and updated annually cultural annual plants, which have very limited data on the aboveground net production, and even less information about the yield of their underground organs. The aim of the research is scientific and theoretical development of crops agriculture in Kuban region also with analysis of land systems and practical mistakes in the agriculture. The development of the agricultural system operation management systems provides a basis to solve the problems of environmental management, their protection, as well as ecological safety at the level of the cultivated land system formation through improving the soil, increasing the vegetation structure complexity, and including corresponding life forms in the vegetation composition. The results of study shows that management of cultivated lands is provided from the outside, where it takes place in a faster way, so it is more reasonable to organize agricultural ecosystems. Besides, the colloidity of wastes of different industries and their role in the formation of complex compost changes the aggregate composition of ordinary chernozem and impacts other aspects of the formation and development of soil and plants in the system of cultivated lands.