In IZMIRAN together with ITEPH the new scientific trend - "System investigation of complex physical phenomena by pattern recognition methods" - has been developed. As a result the principally new system approach for investigaton of complex phusical phenomena is suggested. This approach has been tested on analysis of geomagnitoshperic storms and substorms as integrity in which the set of investigated physical processes of different modality (mechanical, electromagnetic and so on) is considered as a tight interconnected complex in spase and in time (in different phases of development). This approach is applicable to the analysis of the available data about any complex phenomena of solar-terrestrial physics and geophysics. These development of this scientific trend are realized in the form of a number of original scientific works (including two books: И.В.Ковалевский, Ю.И. Морозов. Методы распознавания образов в анализе сложных физических явлений. М., ИЗМИРАН, 1989. - 260с.; 1989.-260c.; J.V.Kovalevsky, Yu.I.Morozov. Pattern Recognition Methods in Analysis of Complex Physical Phenomene.-M.:IZMIRAN,1990.-310p.) of several computer program systems.