The invention discloses an intelligent biogas slurry, water and fertilizer integrated pump station and a working method thereof. The intelligent biogas slurry, water and fertilizer integrated pump station comprises a control cabinet, a first electric adjusting valve, a second electric adjusting valve, a vacuum drainage tank, an EC sensor, a pH sensor, a centrifugal pump and an integrated controller, and the first electric adjusting valve, the second electric adjusting valve, the vacuum drainage tank, the EC sensor, the pH sensor, the centrifugal pump and the integrated controller are arrangedin a control cabinet body; the first electric adjusting valve is in series connection with a biogas slurry inlet pipe stretching into the control cabinet body, the second electric adjusting valve is in series connection with a clear water inlet pipe stretching into the control cabinet body, the output ends of the biogas slurry inlet pipe and the clear water inlet pipe are connected with the vacuumdrainage tank, the output end of the vacuum drainage tank is connected with the inlet end of the centrifugal pump, the outlet end of the centrifugal pump is connected with a mixed solution dischargepipe, and the EC sensor and the pH sensor are connected to the mixed solution discharge pipe. The intelligent biogas slurry, water and fertilizer integrated pump station is high in applicability, andbiogas slurry, fertilizer, water and the like are returned into a field to be recycled; the integration level is high, the system compatibility is strong, and facilities are integrated and free of installation.