The invention discloses an integrated protection system of a transformer substation based on IEC61850. The information about voltage, current and the like of the transformer substation marks GPS clock information by a combination unit; the switch state information of the transformer substation is collected by an intelligent operation box and marks the GPS clock information; and the information about voltage, current and switch state is sent to a protective main station system by Ethernet. The protective main station system judges whether the transformer substation has a failed electrical component according to the uploading information; a tripping operation order is sent to the intelligent operation box by Ethernet if a failure occurs; and the intelligent operation box trips off the corresponding breaker and is insulated from the failure. The protective main station comprises four host computers, wherein, two are used as the main protection for the transformer substation, and the other two are used as the standby protection for the transformer substation. Either host computer of the two used as the main protection can give a tripping operation order if detecting a failure. The twohost computers for the standby protection are directly connected by special network, and can give a tripping operation order if detecting a failure at the same time, so that standby protection misoperation is avoided.