Provided are a control method and system for a cascade hybrid amplifier, in which respective hybrid amplifiers in the cascade hybrid amplifier simultaneously start to implement a pump-starting process comprising: when the hybrid amplifier receives a request to start pumping, determining whether conditions are satisfied, if yes, determining stability of power of an input light of a Raman, starting pumping of an EDFA so that the EDFA enters into an APC operation mode; starting pumping of the Raman, and calculating a gain deviation according to the calculated input light powers before and after pump-starting of the Raman when no reflection alarm exists; and adjusting gain of the Raman according to the gain deviation, and switching to an AGC (automatic gain control) operation mode after the adjustment; and switching the EDFA to the AGC operation mode.