The intentional controlled islanding by intelligent partitioning of the power grid is considered as essential to protect the grid from cascading events, faults, and High Impact Low Probability (HILP) events. To enhance the resilience, stability, and security of the power grid, the proposed model in this paper intentionally divides the affected power network into islands. This paper presents an intelligent partitioning approach to create an islanding solution through multilayer graphs using spectral clustering. The controlled islanding algorithm uses a multi-criteria objective function that considers the correlation coefficients among the frequency of the buses and minimal disturbances in the real and reactive power. The proposed control technique is implemented in two phases. The first phase employs correlation coefficients between frequency of the buses and modularity clustering to identify clusters of coherent buses. During the second stage, all nodes are categorised into groups using Multi-level constrained Spectral Clustering (ML-CSC) to determine the solution for Intentional controlled Islanding that satisfies bus coherency with the minimum level of disruptions to real and reactive power flows across the boundaries. The proposed algorithm for resolving the generator coherency issue and an intelligent islanding solution is demonstrated by simulation experiments conducted on an IEEE 39-bus transmission test system developed in DIGSILENT Powerfactory version 2023. The MATLAB version R2023a is used to construct the ML-CSC control method. The results demonstrated that the proposed ML-CSC algorithm substantially impacts the functioning of the power system, enabling the formation of intelligent islanding during abnormal conditions. Also, the results clearly show that instead of using single-layer spectral clustering, the multi-layer spectral clustering yields a better intentional islanding solution with minimum power flow mismatch which enhances the transient stability of the islands.