Realistic traffic simulation is critical for ensuring the safety and reliability of autonomous vehicles (AVs), especially in complex and diverse urban traffic environments. However, existing data-driven simulators face two key challenges: a limited focus on modeling dense, heterogeneous interactions at urban intersections - which are prevalent, crucial, and practically significant in countries like China, featuring diverse agents including motorized vehicles (MVs), non-motorized vehicles (NMVs), and pedestrians - and the inherent difficulty in robustly learning high-dimensional joint distributions for such high-density scenes, often leading to mode collapse and long-term simulation instability. We introduce City Crossings Dataset (CiCross), a large-scale dataset collected from a real-world urban intersection, uniquely capturing dense, heterogeneous multi-agent interactions, particularly with a substantial proportion of MVs, NMVs and pedestrians. Based on this dataset, we propose IntersectioNDE (Intersection Naturalistic Driving Environment), a data-driven simulator tailored for complex urban intersection scenarios. Its core component is the Interaction Decoupling Strategy (IDS), a training paradigm that learns compositional dynamics from agent subsets, enabling the marginal-to-joint simulation. Integrated into a scene-aware Transformer network with specialized training techniques, IDS significantly enhances simulation robustness and long-term stability for modeling heterogeneous interactions. Experiments on CiCross show that IntersectioNDE outperforms baseline methods in simulation fidelity, stability, and its ability to replicate complex, distribution-level urban traffic dynamics.