Recent studies have combined Mixture of Experts (MoE) and Parameter-Efficient Fine-tuning (PEFT) to fine-tune large language models (LLMs), holding excellent performance in multi-task scenarios while remaining resource-efficient. However, existing MoE approaches still exhibit the following limitations: (1) Current methods fail to consider that different LLM layers capture features at varying levels of granularity, leading to suboptimal performance. (2) Task-level routing methods lack generalizability to unseen tasks. (3) The uncertainty introduced by load imbalance loss undermines the effective specialization of the experts. To address these challenges, we propose HMoRA, a Hierarchical fine-tuning method that combines MoE and LoRA, employing hybrid routing that integrates token-level and task-level routing in a hierarchical manner. This hierarchical hybrid routing allows the model to more efficiently capture both fine-grained token information and broader task contexts. To improve the certainty of expert selection, a novel routing auxiliary loss is introduced. This auxiliary function also enhances the task router's ability to differentiate tasks and its generalization to unseen tasks. Additionally, several optional lightweight designs have been proposed to significantly reduce both the number of trainable parameters and computational costs. Experimental results demonstrate that HMoRA outperforms full fine-tuning across multiple NLP benchmarks, while fine-tuning only 3.9\% of the parameters. The code is available on: https://github.com/LiaoMengqi/HMoRA.