Mobile navigation applications help improve the quality of life and self-confidence of visually impaired people. In order to understand the issues of communication between visually impaired user and mobile navigation application, qualitative analysis related to the structure of navigation process should be used. Therefore we propose a design of new usability evaluation tool that is based on the functional model of a general navigation system for blind. We implemented the tool and evaluated it with data from our recent experiment on mobile navigation aid. Results showed that the tool allows analysis of navigation problems and investigation of specific user behavior, specifically issues related to timing of the navigation dialog in relation to the position of visually impaired user and verification of correct execution of navigation instructions.