Abstract: The subject of this research is the theory and methodology of taxation of natural resource extraction, including raw hydrocarbon materials and solid minerals, approaches towards allocation of tax burden between economic agents, development trends in taxation system of extraction of different types of minerals. Special attention is given to the questions of improvement of tax administration of extractive sector based on implementation of the new digital information technologies of transmitting data on the output of minerals and reform of the institution of declaration of tax. Research methodology includes: consideration of the principles of taxation system of natural resource extraction; determination of interconnection between the elements of this system and its disturbance; formulation of theoretical conclusions on the basis of studying the practice of taxation and tax administration. The scientific novelty consists in identification of vulnerability of taxation system of natural resource extraction from external factors, including world prices for mineral raw materials; substantiation of measures on neutralization of such dependence; proof of the need for harmonization of the key concepts of Taxation Code of the Russian Federation and legislation on the depth, and formation of the system of direct assessment of reasonableness and effectiveness of point-based and categorical incentives on extraction of natural resources. The article substantiates the vectors of reform of tax declaration system regarding the extraction of natural resources and determination of tax liabilities on the records of government reserve of natural resources. An algorithm is developed for organization of direct oil metering at the wells, using the modern digital technologies.