The current single analytical method is difficult to fully diagnose a variety of transformer fault types that may all exist. This paper proposes the integrated use of three classic transformer fault diagnosis. Transformer spectral gas analysis system is introduced to get all kinds of gas first. Then the integrated use of three classic transformer fault diagnosis, including improved three-ratio method, Duval Triangle method and cube graphic method, is applied. The fault diagnosis software that is based on comprehensive analysis method is developed. The fault diagnosis software includes four functional modules, i.e. running state, historical data, diagnostic data and spectra. And the field application proves the validity of transformer fault diagnosis based on the comprehensive analysis.