To solve the problems such as mis-judgment of fault diagnosis of power grid caused by uncertainties, for instance, mis-operation or failure operation of protection and circuit breaker, including transmission error of alarm information, a multi-layer intelligent fault diagnosis method of power grid based on multi-source information fusion is proposed, which includes single-source information diagnosis layer containing switching value diagnosis and electrical quantity diagnosis, and multi-source information fusion diagnosis layer. Finally, a case study of a power grid topology shows that the proposed multi-layer fault diagnosis method can overcome the uncertainties of protection and circuit breaker maloperation, refusal to act and transmission error of alarm information, and accurately identify fault components. The effectiveness and fault tolerance of the proposed method are verified, and it has engineering practical value and good application prospect.