Modern conditions for real investment are generally associated with increasing uncertainty, which is even more relevant when evaluating innovative projects. Current innovation analysis methods using a linear model are outdated. At the same time, an open interactive model of the innovation process, formed due to digitalization, allows to connect to innovations at almost any stage of their life cycle. The aim of the study is to form a methodology for the economic analysis of innovative projects implemented in the context of an open innovation model. To achieve the goal, the study defines approaches to innovation projects differentiation. The approach to the analysis methods selection is based on the decision matrix. The developed decision matrix allows to determine the location of each project as its element and to select analysis methods, considering the project’s uncertainty characteristics. The logic of the analysis methods transformation under the influence of a changing uncertainty level determines the combination of the fuzzy-set approach and the concept of real options. The implementation of the project analysis algorithm leads to the choice of an appropriate method for evaluating effectiveness and ensures that the flexible risk response concept under conditions of improbable uncertainty is taken into account when implementing the option model.