Objective To systematically review the methodological quality of guidelines concerning pharmacological intervention for complicated hypertension. Methods The databases and relevant guideline websites such as MEDLINE, EMbase, CBM, WangFang Data, National Guideline Clearinghouse (NGC), Guidelines International Network (GIN), National Institute for Health and Clinical Excellence (NICE) and Clinical Practice Guideline Network (CPGN) were searched to collect the clinical guidelines concerning pharmacological intervention for complicated hypertension. By adopting the Appraisal of Guidelines for Research and Evaluation (AGREE), the methodological quality of guidelines was assessed. Meanwhile the similarities, differences and features of drug recommendation in guidelines for different areas and diseases were analyzed by means of analogy comparison.Results A total of 21 guidelines concerning pharmacological intervention for complicated hypertension were included. The number of guidelines concerning hypertension complicated with coronary heart disease (CHD), stroke, diabetes mellitus (DM) and kidney disease (KD) was 5, 5, 7 and 4, respectively. The publication year ranged from 2000 to 2011. According to the AGREE instrument, 19 and 2 guidelines were graded as Level B and C, respectively. The overall guidelines got low average scores in the domain of “Stakeholder involvement” and “Applicability”, including 9 evidence-based guidelines. There were totally 4 and 3 classes in terms of the level of evidence and recommendation, respectively; moreover, 10 and 6 expression forms were adopted in the level of evidence and recommendation, respectively. For hypertension with angina pectoris, -blocker (BB) and calcium channel blocker (CCB) were recommended unanimously. For hypertension with myocardial infarction, angiotensin converting enzyme inhibitor (ACEI) and BB were recommended unanimously. For hypertension with heart failure, ACEI, angiotensin-receptor blocker (ARB) and BB were recommended unanimously. For hypertension with later stage of post-stroke, 76.47% guidelines recommended diuretic (D) and ACEI. For hypertension with acute stroke, recommendations were mainly based on the guidelines developed by American Heart Association/American Stroke Association (AHA/ASA). For hypertension with DM or KD, the guidelines basically recommended that systolic/diastolic pressure should be controlled in the range of less than 130/80 mmHg. For hypertension with DM, ACEI were recommended unanimously, followed by D and CCB. For hypertension with KD, ACEI/ARB was recommended, while 3 of the 5 guidelines recommending CCB were from Asian. Conclusion The overall methodological qualities of complicated hypertension guidelines differs, with high proportion of evidence-based guidelines. The classification criteria of the levels of evidence and recommendation are still suboptimal. For hypertension with CHD, DM, KD and later stage of stroke, results from high quality clinical evidence are consistent, and the recommendations are basically unanimous, with no regional and quality difference. But in some clinical researches beyond reaching a consensus at present, the recommendation discrepancy exists, and there still remains controversy for hypertension with acute stroke.