A number of probabilistic methods for aircraft conflict evaluation are presented. The analytical method is shown. The probability method that enables taking into account the features of stochastic dynamics of motion and the new compositional method of conflict probability evaluation are proposed. The feature of this method is that analytical solution is made using the predicted uncertainty areas of each aircraft position separately, making it possible to manage the position uncertainty and to apply for a wider range of scenarios. The multi-criteria decision-making for conflicts resolution is discussed. Optimality criteria and constraints for conflict resolution are defined. The generic multi-criteria model of conflict-free trajectories selection and the methods of resolution of two- and multi-aircraft conflicts have been developed. These methods provide the synthesis of conflict-free trajectories using different aircraft maneuvers according to criteria of flight regularity, economy, and maneuvering complexity using the multi-criteria dynamic programming.