Naïve CD4+ T cells can be differentiated into T helper cells through several rounds of division, and these differentiated T helper cells are essential for human immune activities such as infection, allergic responses, macrophages and also mediate direct antiviral function. Here, we analyzed the proteins involved in signal transduction of early T cell differentiation by setting each time point divided into 6 time points. The samples were labeled by using TMT-reagent after digestion and the labeled peptides were subjected to LC-MS/MS analysis. After integrating RNA-seq, global and phosphorylated proteome profiling, we characterized the network of early signaling pathways for T cell differentiation. Through the analysis of transcriptomes based on RNA-seq, we classified networks of transcription factors of T cell differentiation. And we identified 847 differentially phosphorylated peptides from phosphoproteomic analysis and 755 differentially expressed proteins from global proteomics. All DEPs (fold changes>3) among each analysis were identified in the abundance of each time point to perform gene ontology and pathway analysis. In conclusion, our results and future experiment will be able to identify the modeling of drugs related to CD4 activation and T cell differentiation and also identify autoimmune diseases caused by T cell mutation.