The article presents the features of innovative projects of industrial enterprises that complicate the process of their management. The main groups of mathematical methods used to manage innovative projects are identified. The possible directions of further developing mathematical methods in the field of managing the complex innovative projects at industrial enterprises are determined. Algorithms of accounting the influence of uncertainty factors on the duration and costs that associate with implementing the innovation project works are presented. A distinctive feature of these algorithms is the usage of fuzzy production rules. These rules formulate recommendations for managing these projects based on the distribution of resources available in the organization depending on the results of each stage. It allows minimizing the execution time, both individual stages, and the entire innovation project as a whole. The variant of information support formation is offered that is presented in the form of a physical model of the database. This model allows storing all the information available in the industrial organization that necessary to manage these projects. A distinctive feature of this database is the ability to store information on the impact of uncertainties on the implementation effectiveness in a formalized form. This information is necessary for the implementing the developed algorithms.