To address the challenge that the existing methods struggle to balance solution efficiency, assignment quality, and generalization in airport gate pre-assignment at large hub airports under dynamic changes in flight number, gate layout, and assignment rules, an airport gate assignment algorithm based on node prediction in conflict graph of assigned activities was proposed. Firstly, an airport gate assignment model was established with the objectives of maximizing gate assignment rate and cumulative soft preference. Secondly, the feasible airport gate assignment activities were screened through an airfield zoning strategy, the corresponding conflict graph of assignment activities was constructed, the Node-Edge Collaborative Updating Graph Neural Network (NECU-GNN) was designed, and the NECU-GNN for Node Prediction model (NECU-GNN4NP) was developed. Finally, the NECU-GNN4NP-guided ranking-based Max Weighted Independent Set Algorithm (MWISA) was proposed on the basis of NECU-GNN4NP, so as to solve the optimal set of assignment activities for the conflict graph of assignment activities and obtain the airport gate assignment scheme. Experimental results based on Shenzhen Bao’an International Airport data show that compared with the current optimal assignment scheme at Shenzhen Bao’an International Airport, the proposed algorithm increases the gate assignment rate by 4.2, 4.3, and 3.1 percentage points, respectively, improves the cumulative soft preference by 38.1%, 30.3%, and 42.8%, respectively, and reduces the solution time by 65.3%, 39.1%, and 41.4%, respectively, in low-peak, normal, and high-peak scenarios. In addition, migration experimental results based on Yinchuan Hedong International Airport data demonstrate that the proposed algorithm can be adapted and applied to other airports rapidly. It can be seen that the proposed algorithm not only has good generalization but also enables efficient and high-quality airport gate assignment.