Compared with single-target drugs, multitarget drugs may improve the safety and efficacy of the treatment of multifactorial diseases. However, few multitarget drugs are on the market or in clinical trials currently, and multitarget small molecules account for the majority. Compared with multitarget small molecules, multitarget peptides have unique advantages and show good effects in a variety of diseases. This article discusses the design process of multitarget peptides in four aspects, including target combination, peptide selection, lead generation, and lead optimization. In addition, we analyzed in detail the research cases of multitarget peptides for several multifactorial diseases over years, aiming to reveal the trends and insights of the potential uses of multitarget peptides.