Human milk (HM) is the golden standard of infant nutrition that can protect immature body function and enhance nutrition metabolism to ensure infant growth. Region specificity and lactation period could change the protein composition in HM. In this research, proteomics analysis was used to compare proteomes across eight cities, namely Harbin, Lanzhou, Guangzhou, Chengdu, Jinhua, Weihai, Zhengzhou, and Beijing, which represented the northeast, northwest, southeast, southwest, east, and north and central regions of China,. Proteins varied significantly among the cities. These different proteins were mainly involved in the process of platelet degranulation, innate immune response, and triglyceride metabolic process, which might be due to different living environments. These differences also lead to variation in protection and fat metabolism from mothers to infants in different cities. Four proteins were expressed differently during 6 months of lactation, namely Dipeptidyl peptidase 1, Lysozyme C, Carbonic anhydrase 6, and Chordin-like protein 2. The changes in these proteins might be because of the change of growth needs of the infants. The findings from our results might help to improve the understanding of HM as well as to design infant formula.