Smart substation is an important part of smart grid. The safe and stable operation of the grid cannot be separated from the protection equipment. Therefore, it is necessary to optimise the protection control system of substation. Hierarchical protection of power grid includes three levels: prefecture level protection, station area protection and wide area protection. The technology of hierarchical protection is the inevitable product of smart grid development process which is characterized by informatization, automation and interaction. Compared with traditional relay protection, the system has great changes in principle and implementation mode, and its performance also has great progress. In this paper, a new generation of Smart substation hierarchical protection control system architecture is discussed. And the configuration scheme and coordination scheme are proposed to achieve the coordination and unity of relay protection and safe control, in order to adapt to the trend of power grid interconnection and complex, changeable operation requirements. Combining with a practical case of 110kV substation, this paper analyses the protection configuration scheme at prefecture level and station level, and puts forward the optimisation and integration scheme of interval layer equipment and process layer equipment.