The problems of synthesis and analysis of multidimensional controlled models of population dynamics are of both theoretical and applied interest. The need to solve numerical optimization problems for such a class of models is associated with the expansion of ecosystem control requirements. The need to solve the problem of stochastization is associated with the emergence of new problems in the study of ecological systems properties under the influence of random factors. The aim of the work is to develop a new approach to studying the properties of population dynamics systems using methods of numerical optimization, stochastization and machine learning. The synthesis problems of nonlinear three-dimensional models of interconnected species number dynamics, taking into account trophic chains and competition in prey populations, are studied. Theorems on the asymptotic stability of equilibrium states are proved. A qualitative and numerical study of the models is carried out. Using computational experiments, the results of an analytical stability and permanent coexistence study are verified. The search for equilibrium states belonging to the stability and permanent coexistence region is made using the developed intelligent algorithm and evolutionary calculations. The transition is made from the model specified by the vector ordinary differential equation to the corresponding stochastic model. A comparative analysis of deterministic and stochastic models with competition and trophic chains is carried out. New effects are revealed that are characteristic of three-dimensional models, taking into account the competition in populations of prey. The formulation of the optimal control problem for a model with competition and trophic chains is proposed. To find optimal trajectories, new generalized algorithms for numerical optimization are developed. A methods for the synthesis of controllers based on the use of artificial neural networks and machine learning are developed. The results on the search for optimal trajectories and generation of control functions are presented.The obtained results can be used in modeling problems of ecological, demographic, socio-economic and chemical kinetics systems.