The article is devoted to methodological questions in research on the development of agriculture on the basis of objective cyclical-genetic regularities using mathematical-economic models. This approach is necessary to solve the problem of ensuring food security of the country on the basis of innovative development of the agro-industrial complex. Influence of long waves of Kondratiev on development of agriculture of Russia during implementation of agrarian reforms is analyzed. Existence of long cycles in agriculture lasting 64 years is for the first time proved and factors of innovative development of agriculture are revealed. Considered are the main types of innovations in agriculture and implemented forecasting cyclical development of the agrarian sectoruntil 2042.