Methamphetamine (Meth) withdrawal elicits anxiety, which is a public health concern with limited therapeutic options. Previous studies implied a strong correlation between mPFC and Meth withdrawal. Here, we examined the role of Gegen‐Qinlian decoction (GQD) in Meth withdrawal anxiety and explored potential therapeutic targets in mPFC. We found that intra‐gastric administration of GQD during the withdrawal period efficiently alleviated anxiety‐like behaviours in Meth‐withdrawn mice. Further, GQD could restore Meth withdrawal‐triggered pathway of GABAergic interneurons (GABA IN)‐pyramidal neurons (PN) in the mPFC of Meth‐withdrawn mice, especially the prelimbic cortex (PrL) sub‐region and PV‐positive GABA IN. While, GQD had no obvious effects on the glial cells in the mPFC of Meth‐withdrawn mice. By transcriptomic analysis and validation of several gene candidates, we found that genes in the MAPK signalling pathway, especially those related to heat shock proteins, including Hspa1a, Hspa1b and Hspb1, might be GQD‐targeting genes in mPFC to treat Meth withdrawal anxiety, as indicated that these genes were up‐regulated by Meth withdrawal but rescued by GQD in mPFC. Collectively, our findings identified for the first time that GQD could efficiently alleviate Meth withdrawal anxiety, partially through regulating the local GABA IN‐PN pathway and transcriptomic profile of mPFC. The present study confirms that TCM, such as GQD, will be a desirable therapeutic approach in the treatment of drug addiction and related emotional deficits.