Codonopsis pilosula is a valuable plant used for both food and medicinal purposes. However, fresh C. pilosula is prone to spoilage due to microbial infection, which can significantly reduce its medicinal value and lead to the accumulation of mycotoxins. To address this, various storage methods were tested over 30 days, including conventional drying, vacuum refrigeration, atmospheric refrigeration, vacuum storage at room temperature, quick-freezing, conventional freezing, lyophilization, chitosan, lysozyme, and phytic acid. The refrigerated, frozen, lyophilized, and lysozyme groups remained unspoiled. Flavonoids, the most abundant compounds in C. pilosula, were best preserved in the lyophilized samples. Importantly, lyophilized C. pilosula retained the ability to activate CD4+ T cells, which is crucial for its anti-tumor effects. Luteolin, a key active component with immunomodulatory effects in C. pilosula, can activate CD4+ T cells to inhibit tumors. In conclusion, lyophilization maximizes the retention of total flavonoids and helps maintain immune-regulatory functions.