The main task of agro-industrial production is to provide the population with food products for the production of which energy is expended in the form of electricity, technical means, fuels and lubricants, mineral fertilizers, etc. Accordingly, we have developed a concept and general methodological principles for the analysis of ecological and biotechnical systems in animal husbandry, it makes it possible to simulate the influence of various factors on the energy and ecological efficiency of systems, to compare and search for energy-saving modes and technologies. General methodological principles have been developed for the analysis of energy efficiency and environmental safety of agricultural ecological and biotechnical systems, which are based on the definition of the bioenergy efficiency coefficient, the quantitative expression of which is the ratio of energy accumulated in products to the total energy consumption for its production. This makes it possible to model with sufficient accuracy the influence of various factors on the energy and environmental efficiency of the system, to compare and search for energy-saving modes and technologies in order to find and select the most energy efficient ones to increase the energy efficiency of the complex.