The process of evaluating the effectiveness, speed, and general capabilities of a computer system that is embedded inside a larger device or system and created for a particular purpose is known as embedded computer performance evaluation. Specialized computing systems called embedded systems are built into a wide range of gadgets, including medical, industrial, , automotive and consumer electronics. In this manuscript, Optimized Meta-path extracted graph neural network for embedded computer performance evaluation model(MEGNN-EC-PEM) is proposed. Initially, the input data is obtained from real-time sensor measurements and system metrics for model training and testing. The input image is pre-processed using Orthogonal Master-slave Adaptive Notch Filter (OMANF) and it removes the noise from the collected data. Then, the pre- processed data are fed to embedded computer performance using Meta-path extracted graph neural network (MEGNN). In general, MEGNN does not express adapting optimization techniques to determine optimal parameters to assure precise embedded computer performance evaluation model. Hence, the Hunter–prey optimization algorithm (HPOA) is used to optimize Meta-path extracted graph neural network which accurately categorized embedded computer performance. Then, the proposed MEGNN-EC-PEM is implemented and the performance metrics like Modelling Accuracy, latency, Throughput, memory cost and Energy Consumption are analyzed. The performance of the MEGNN-EC-PEM approach attains 19.41%, 20.08% and 32.57% higher modelling accuracy, 22.41%, 23.08% and 24.57% lower latency and 23.01%, 23.08% and 24.07% higher throughput when analyzed through existing techniques like a state-based modelling approach for effective performance evaluation of embedded system architectures at transaction level (SMA-EPE-ESAT), Evaluating the performance of pre-trained convolutional neural network for audio classification on embedded schemes for anomaly detection in smart cities (PCNN-ACES-ADSC) and Animal behaviour classification via deep learning on embedded systems (ABC-VDL-ES) methods respectively.