The purpose of the study is to develop tools for improving the system of rational land use in agriculture in the Krasnodar Territory of Russia. The work is based on methods of system analysis, logical modeling, expert assessments, calculation and design and others. Theoretical and methodological approaches to organizing a system of rational land use in agriculture have been refined to emphasize the necessity of innovative development. This development should be founded on a harmonious integration of economic and environmental considerations, while also accounting for social factors that ensure employment and enhance the quality of life for the rural population. The constituent elements of innovative systems of rational land use include methods of biological and organic farming, intelligent agriculture, robotic crop production based on multi-storey agro-complexes, and ecosystem modeling technologies. It was established that between 2018 and 2023, the efficiency of land and resource utilization in agriculture within the Krasnodar Territory significantly improved, as evidenced by a more than twofold increase in productivity per hectare, reflected in the revenue and profit generated from the sale of agricultural products per hectare of cultivated land. The profitability of crop production for the analyzed period fluctuated in the range from 31.1 to 48.2%. A forecast was made for the development of elements of the rational land use system and the efficiency of the implementation of the land-resource potential of crop production of agricultural organizations in the region for 2030, assuming inertial and innovative options, which were distinguished by different rates of innovative transformations in the industry. By 2030 the innovative development option demonstrated an increase in the volume of production of crop products, an increase in hectare productivity, calculated based on profit up to 65.2 thousand rubles per 1 hectare and the level of profitability of crop production up to 52.9%.