The complexity and diversity brought by the distributed architecture of the new generation electric information collection system have deepened the difficulty of constructing evaluation verification index systems and quality evaluation models. Moreover, the presence of differentiated components has made fair and scientific verification challenging. Therefore, leveraging graph neural networks and siamese networks, a integrated construction quality evaluation system based on comprehensive weighted assessment in multiple scenarios was developed. Firstly, a graph neural network was constructed based on terminal data of the branches electricity usage information collection system and the link topology structure. Subsequently, this network was deployed on the headquarters side to directly acquire terminal data and generate mirror network input from the branches data, enabling real-time acquisition of various system operational indicators. Finally, the similarity between the headquarters and branches data was calculated using siamese networks to compute accuracy compensation weights for checking and evaluating various indicators, thereby obtaining comprehensive weighted quality evaluation indicators of the branches new generation electric information collection system. We use three types of services including electricity data collection, load forecasting, and task scheduling as experimental scenarios. The results showed that the multidimensional comprehensive weighted quality assessment combined with accuracy compensation obtained from the siamese network resulted in business construction quality assessment values of 97.92%, 95.95%, and 99.96% in branch. This value is approximately equal to the quality evaluation value of manual work, so the method can effectively verify the construction quality of new systems in the branch.