Student performance prediction has attracted increasing attention in the field of educational data mining, or more broadly, intelligent education or “AI + education”. Accurate performance prediction plays a significant role in solving the problem of a student dropping out, promoting personalized learning and improving teaching efficiency, etc. Traditional student performance prediction methods usually ignore the potential (underlying) relationship among students. In this paper, we use graph structure to reflect the students’ relationships and propose a novel pipeline for student performance prediction based on newly-developed multi-topology graph neural networks (termed MTGNN). In particular, we propose various ways for graph construction based on similarity learning using different distance metrics. Based on the multiple graphs of different topologies, we design an MTGNN module, as a key module in the pipeline, to deal with the semi-supervised node classification problem where each node represents a student (and the node label is the student’s performance, e.g., Pass/Fail/Withdrawal). An attention-based method is developed to produce the unified graph representation in MTGNN. The effectiveness of the proposed pipeline is verified in a case study, where a real-world educational dataset and several existing approaches are used for performance comparison. The experiment results show that, compared with some traditional machine learning methods and the vanilla graph convolutional network with only a single graph topology, our proposed pipeline works effectively and favorably in student performance prediction.