A new generation of smart substation has become the future of substation. At present, the reliability assessment method of a new generation of smart substation is based on substation system or relay protection system separately, without considering the comprehensive influence of this two systems, resulting that high reliability index are obtained. Based on minimum path algorithm, firstly, this paper establishes the reliability model of a new generation of smart substation relay protection system. Then, the equivalent index considering the comprehensive influence of the primary system and relay protection system is put forward. And a new generation of smart substation reliability is evaluated by the above model and the equivalent index. Finally, an example is given to verify the effectiveness of the proposed method. This work is supported by Science and Technology Program of State Grid Hubei Electric Power Company (No. 15KJ020602D20042).