Macro-conditions changes associated with technological patterns shift leads to the transformation forms of interaction between individual industrial enterprises. At the same time, they themselves, as well as their counterparties, are changing. The subjects of interaction become more complicated, the number of connections between them and their goals increases. The indisputability of innovations for the structural transformation of industrial systems at the present stage is indisputable. Existing methodological tools for choosing a strategy for such cooperation no longer meet the requirements of the subjects and the environment themselves, which determines the relevance of developing diagnostic methods and choosing a strategy for development of industrial enterprises within the framework of joint innovative processes implementation. This article substantiates the need to develop methodological aspects of current state diagnostics of industrial enterprises interaction, which makes it possible to identify “critical” areas in their functioning and identify the most optimal directions of their development, which will make it possible to substantiate strategic priorities for the development of the innovation sphere of the region and ensure the systematic nature of the coordinated innovation policy in its scientific and industrial sector. Based on the identified groups of factors, the stages of methodology implementation were described, at each of which the most appropriate methods were justified and the developed proposals for them were presented.