Efficient deployment of large language models, particularly Mixture of Experts (MoE), on resource-constrained platforms presents significant challenges, especially in terms of computational efficiency and memory utilization. The MoE architecture, renowned for its ability to increase model capacity without a proportional increase in inference cost, greatly reduces the token generation latency compared with dense models. However, the large model size makes MoE models inaccessible to individuals without high-end GPUs. In this paper, we propose a high-throughput MoE batch inference system, that significantly outperforms past work. MoE-Lightning introduces a novel CPU-GPU-I/O pipelining schedule, CGOPipe, with paged weights to achieve high resource utilization, and a performance model, HRM, based on a Hierarchical Roofline Model we introduce to help find policies with higher throughput than existing systems. MoE-Lightning can achieve up to 10.3x higher throughput than state-of-the-art offloading-enabled LLM inference systems for Mixtral 8x7B on a single T4 GPU (16GB). When the theoretical system throughput is bounded by the GPU memory, MoE-Lightning can reach the throughput upper bound with 2-3x less CPU memory, significantly increasing resource utilization. MoE-Lightning also supports efficient batch inference for much larger MoEs (e.g., Mixtral 8x22B and DBRX) on multiple low-cost GPUs (e.g., 2-4 T4).