The invention discloses a method of recovering a compound fertilizer from polishing cleaning wastewater in aluminum industry and system configuration. A high pressure atomizing spray tank, a second immobile washing tank and a first immobile washing tank successively communicate. The high pressure atomizing spray tank is connected to a storage tank for storing spraying wastewater, and the high pressure atomizing spray tank communicates to the second immobile washing tank; an aluminium phosphate recovery system comprises a reaction tank, a #5 pump, a liquid ammonia tank and a filter press, the reaction tank communicates to a #1 pump, and an N-P compound fertilizer recovery system comprises a recovery tank, a #7 pump and a filter communicate successively. The invention also discloses a methodof recovering the compound fertilizer from a polishing solution. By adopting the washing tank to intercept the polishing solution for centralized treatment, the trouble of treating the massive wastewater mixed with other water is avoided, the environment-friendly cost of treating phosphorus and ammonia-nitrogen containing wastewater is lowered greatly, and discharge of nickel-containing solid hazardous wastes is reduced greatly. By adopting the high pressure atomizing spray tank, the recovery amount of the waste liquor is reduced.