The object of research is the reliability level of non-invasive complex spectral-binary diagnostics using the «Quanton» method. One of the most problematic issues of this method is ensuring a given reliability level of diagnostic results with the maximum process performance. In the course of the research, logical-mathematical models of a typical problem of structural-parametric optimization and methods of increasing the reliability were used, providing for the repetition of measurements and the introduction of an additional channel for obtaining information. The model of the general criterion for the reliability of the information obtained in the diagnostic process is presented taking into account the probabilities of errors in obtaining information from two independent channels (spectral and binary) and the possibility of its repetition. To calculate the performance, an additive dependence is proposed, which takes into account the sequence of operations and the structuredness of the total length of time for the main, preparatory and final parts. Based on the obtained dependencies, the problem of optimizing the diagnostic process by the maximum value of the performance criterion under the constraints on the reliability level of its results and the number of measurements from one biologically active zone is posed and solved. It is established that the diagnostic process according to the «Quanton» method, which consists of two operations and is optimized by the performance criterion, has sufficiently broad possibilities to influence the reliability level of its results. This level is provided by the original measurement accuracy and the availability of repeated measurements. With real, fairly broad values of the output errors of the spectral and binary diagnostics processes, by repeating the measurements, the total error of the method can be reduced by a factor of 10 or more. According to the proposed dependencies, it is possible to perform an analysis of the suitability of various technical means used in spectral and binary diagnostics, by the reliability level and by the level of process performance. It is also possible to determine the feasibility of introducing an additional channel for obtaining information. Due to obtaining high reliability of diagnostic information, it is possible, based on the «Quanton» method, to determine the most optimal effect on physiological processes in a living organism with the aim of correcting them. At the same time full non-invasiveness, safety and high efficiency in a short period of time are ensured.