Efficient reproductive management of dairy cows depends primarily upon accurate estrus identification. However, the currently available estrus detection methods, such as visual observation, are poor. Hence, there is an urgent need to discover novel biomarkers in non-invasive bodily fluids such as milk to reliably detect estrus status. Proteomics is an emerging and promising tool to identify biomarkers. In this study, the proteomics approach was performed on milk sampled from estrus and non-estrus dairy cows to identify potential biomarkers of estrus. Dairy cows were synchronized and timed for artificial insemination, and the cows with insemination leading to conception were considered to be in estrus at the day of insemination (day 0). Milk samples of day 0 (estrus group) and day −3 (non-estrus group) from dairy cows confirming to be pregnant were collected for proteomic analysis using the tandem mass tags (TMT) proteomics approach. A total of 89 differentially expressed proteins were identified, of which 33 were upregulated and 56 were downregulated in the estrus milk compared with the non-estrus milk. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that acetyl coenzyme A carboxylase α (ACACA), apolipoprotein B (APOB), NAD(P)H steroid dehydrogenase-like (NSDHL), perilipin 2 (PLIN2), and paraoxonase 1 (PON1) participated in lipid binding, lipid storage, lipid localization, and lipid metabolic process, as well as fatty acid binding, fatty acid biosynthesis, and fatty acid metabolism, and these processes are well documented to be related to estrus regulation. These milk proteins are proposed as possible biomarkers of estrus in dairy cows. Further validation studies are required in a large population to determine their potential as estrus biomarkers.