Some problems are confronted in the development of Chinese medicine (CM) evidence-based clinical practice guidelines in the aspects of individualized treatment, quality of research, reporting bias, safety assessment, and so on. After comprehensive retrieving of current methods for developing evidence-based clinical practice guidelines in the field of complementary and alternative medicine, and an optimal combining with widely accepted standardized methods in evidence-based clinical practice guidelines for allopathic medicine, we put forward strategies for these aforesaid problems. In terms of individualized treatment, practical randomized control trials could be considered for inclusion. In terms of quality of research, the method to formulate guideline recommendations was proposed in case of insufficient evidence. In terms of reporting bias, commonly used databases in complementary and alternative medicine were listed. In terms of safety evaluation, GRADE system was suggested to adopt.