The study of different types of complex dynamical systems (technical, biological, social, economical) has attracted the attention of many researchers for a long time already [1–4]. Important direction of such a study is development of methods for evaluation of state, operating quality, and interaction between objects of those systems [5–10]. Among main problems arising in this case local and global evaluation of complex dynamical systems quality [10, 11] may be pointed out, as well as determination of their optimal operation modes [12], analysis of system behaviour during a certain period of time, and the choice of optimal operating system out of certain class of equivalent systems. We propose a unified approach to solving the above-listed problems. It is based on their comprehensive (which presupposes consideration of as many characteristics of system’s elements as possible), multicriteria, and multiparameter analysis. In order to provide operative processing of results the developed evaluation is multilevel, which means formulation of conclusions of different generalization degrees: from locally determining the behaviour of particular characteristics of system’s elements to finally determining quality of its operation in general. Problems considered in this paper and methods for their solution are illustrated with example of motion analysis of man’s musculoskeletal system (MMSS) with prosthetic lower limb [13–15].