Glucocorticoids are commonly used in anti-inflammatory and immunomodulatory therapies, but glucocorticoid withdrawal can result in life-threatening risk of adrenal insufficiency. Chinese patent pharmaceutical product Jinkui Shenqi (JKSQ) pill has potent efficacy on clinical adrenal insufficiency resulted from glucocorticoid withdrawal. However, the underlying molecular mechanism remains unclear. We used an animal model to study JKSQ-induced metabolic changes under adrenal insufficiency and healthy conditions. Sprague-Dawley rats were treated with hydrocortisone for 7 days, with or without 15-day JKSQ pre-treatment. Sera were collected after 72-hour hydrocortisone withdrawal and used for global and free fatty acids (FFAs)-targeted metabolomics analyses using gas chromatography/time-of-flight mass spectrometer (GC/TOFMS) and ultra-performance liquid chromatograph/quadruple time-of-flight mass spectrometer (UPLC/Q-TOFMS). Rats without hydrocortisone treatment were used as controls. JKSQ pre-treatment normalized the significant changes of 13 serum metabolites in hydrocortisone withdrawal rats, involving carbohydrates, lipids and amino acids. The most prominent effect of JKSQ was on the changes of FFAs and some [product FFA]/[precursor FFA] ratios which represent estimated desaturase and elongase activities. The opposite metabolic responses of JKSQ in adrenal insufficiency rats and normal rats, highlighted the “ Bian Zheng Lun Zhi” (treatment based on ZHENG Differentiation) guideline of TCM, and suggested that altered fatty acid metabolism was associated with adrenal insufficiency after glucocorticoid withdrawal and the protective effects of JKSQ.