This paper investigates the multi-agent cooperative exploration problem, which requires multiple agents to explore an unseen environment via sensory signals in a limited time. A popular approach to exploration tasks is to combine active mapping with planning. Metric maps capture the details of the spatial representation, but are with high communication traffic and may vary significantly between scenarios, resulting in inferior generalization. Topological maps are a promising alternative as they consist only of nodes and edges with abstract but essential information and are less influenced by the scene structures. However, most existing topology-based exploration tasks utilize classical methods for planning, which are time-consuming and sub-optimal due to their handcrafted design. Deep reinforcement learning (DRL) has shown great potential for learning (near) optimal policies through fast end-to-end inference. In this paper, we propose Multi-Agent Neural Topological Mapping (MANTM) to improve exploration efficiency and generalization for multi-agent exploration tasks. MANTM mainly comprises a Topological Mapper and a novel RL-based Hierarchical Topological Planner (HTP). The Topological Mapper employs a visual encoder and distance-based heuristics to construct a graph containing main nodes and their corresponding ghost nodes. The HTP leverages graph neural networks to capture correlations between agents and graph nodes in a coarse-to-fine manner for effective global goal selection. Extensive experiments conducted in a physically-realistic simulator, Habitat, demonstrate that MANTM reduces the steps by at least 26.40% over planning-based baselines and by at least 7.63% over RL-based competitors in unseen scenarios.