The article includes the solution of the question of methodical ware institutional changes research relating to different markets. Relying on the former suggested theoretical approach and the relevant modelling the article describes a set of techniques developed by the authors, designed for practical assessment of the economic efficiency of institutional changes in the markets. The complex consists of four interrelated methods: the boundary market delimitation; the allocation of market economic subjects and the description of the institutional environment of the market; the signification of institutional changes on the market; the analysis of institutional changes and calculation of their efficiency in the market; the decision making on rising of institutional change efficiency. A key pillar of the methodology for determining of the market boundaries, the allocation of economic subjects of the market and the description of the institutional environment of the market is a logical scheme of signification of institutional changes subjects. As part of the methodology of institutional changes signification, a shaping circuit of a new institutional environment of the market is developed, a sequence of changes entering in the functional institution is formed, and then the influence of changes in the components of the functional institution on the subject of activity and institutional changes is determined. The method of institutional change analysis and calculation of their efficiency consists of the relevant circuit and an evaluation method. The decision-making method for the efficiency rising of institutional changes proposes the decision-making circuit, which is applicable, both at the stage of designing and discussion of the new Institute, and at the stage of its implementation and operation.