In view of the urgency of the problem of cancer diseases of the vocal apparatus and their treatment by surgery relevance of speech rehabilitation of patients is increased. This article describes the phoneme pronunciation quality assessment system, its inputs, outputs and internal parameters. Presented a mathematical model of the system, a functional model of the system in the form of contextual diagrams and decomposition of the 1st level of IDEF0 diagram. Also presented an algorithm of phoneme assessment in comparison with a certain set of reference phoneme. Was proved the accuracy and adequacy of the proposed system in comparison with expert judgment.