The invention discloses a comprehensive compensation system for a Vv wiring traction substation with out-of-phase and in-phase compatibility. On the secondary side of a traction substation, both a leading phase (T1-N) and a lagging phase (T2-N) supplies a traction load with power. The direct current sides of a first static var generator (SVG1) and a second static var generator (SVG2) are arranged in a back-to-back way, the alternating current sides of the SVG1 and the SVG2 are respectively connected with the leading phase (T1-N) and the lagging phase (T2-N) of a Vv traction transformer, the comprehensive compensation system which is compatible with out-of-phase and in-phase structures and easily develops and transforms from an out-of-phase mode to an in-phase mode is formed so as to generate a negative sequence power flow opposite to the traction load, and reactive compensation and harmonic suppression are combined through reasonable control. The application of the system is flexible, in-phase power supply is easy to realize, power phase splitting at the exit part of the traction substation is cancelled, and power supply bottleneck is eliminated.