The invention relates to a dual failures fault isolation method and system for a circuit breaker of a bus protection device. The method comprises the steps of firstly judging whether the bus protection device has an action of jumping to a main transformer branch; if yes, then calculating a main transformer branch current and a bus voltage, and judging whether a condition of main transformer branch circuit breaker failure is satisfied; and when the current of a certain phase of the main transformer branch satisfies a failure criterion and the duration is greater than a setting time delay, the main transformer circuit breaker failure protection has an action of jumping to a high voltage side, a medium voltage side and a low voltage side of the main transformer in a united way. The double failure fault isolation method for the circuit breaker of the bus protection device provided by the invention solves the problem of starting remote backup protection by mistake due to local backup action resistance when dual failures of the circuit breaker occur, thereby reducing the damage of the failures to electrical equipment and effectively ensuring the safe and stable operation of the whole power grid. In addition, the dual failures fault isolation method provided by the invention adopts a manner of combining a full-wave fourier algorithm and a cosine difference algorithm to distinguish the main transformer branch circuit breaker failure, thereby effectively restraining the influence of CT current trailing on circuit breaker failure protection when the failures are removed, and improving the reliability of the protection action.