The intelligent algorithm for building prediction mathematical models using self-organization method was discussed in this paper. This method is one of the key points in modern intelligent system based on theory of functional systems for establishing pre-diction model of control objects. For avoiding shortcoming of traditional self-organization method requiring enormous computing re-source, the modified algorithm combining DEMARK trend and self-organization method was proposed, based on which the predic-tion model of error parameters of navigation system was constructed. Simulation research on application of the given algorithm in prediction of errors of navigation systems shows the effectiveness of this algorithm on building prediction model in aerocraft intelli-gent control system.