Chiplet-based 3DICs have emerged as modular solutions for large-scale, high-performance computing systems. However, unlike monolithic Network-on-Chips (NoCs), 3DICs using active interposers encounter difficulties in managing heterogeneous and high-load network traffic patterns. The emerging field of Networks-on-Active-Interposer (NOAI), independently designed from top dies’ interconnects, is desired to address these challenges by supporting flexible topologies, low-latency memory access, and reduced traffic congestion. To satisfy the requirements, we propose a heterogeneous dual-layer interconnect architecture, EIGEN, for chiplet-interposer systems, along with a reinforcement learning (RL)-based routing framework, which can provide efficient and flexible communication for chiplet-based 3DICs. EIGEN features an application-aware switch-programable interconnection layer (AspLayer) and a dynamic packet-routing interconnection layer (DynLayer) on the interposer, respectively. To optimize inter-chiplet data communication, we also develop an RL-based path routing framework tailored to this dual-layer architecture. The RL framework’s state space includes topology, network, and memory metrics, while the RL reward is set as the product of average packet latency and link utilization. The effectiveness of EIGEN is demonstrated through different applications where CPU, GPU, and AI accelerator chiplets are integrated via NOAI. Simulation results show that the proposed EIGEN achieves up to $\mathbf{6 7. 1 6 \%}$ latency reduction, $\mathbf{5 3. 8 9 \%}$ hops reduction and $\mathbf{1 1. 2 1 \%}$ runtime reduction compared to the state-of-the-art (SOTA) chiplets interconnect architectures. Furthermore, sensitivity analysis of network scaling shows that the EIGEN architecture and framework exhibit strong scalability, with latency reduction of $\mathbf{2 0. 9 6 \%}$ to $\mathbf{5 2. 7 7 \%}$ and hop reduction of $\mathbf{1 9. 7 2 \%}$ to $\mathbf{4 3. 4 1 \%}$ as the system scales from $4 \times 4$ to $32 \times 32$ chiplets.