A series of novel N2-phenyl-N4-5-(dimethylphosphinyl)-6-quinoxalinaminepyrimidine-2,4-diamine derivatives were synthesized and evaluated as potential inhibitors of EGFR C797S-mediated resistance. Notably, most of these compounds exhibited robust antiproliferative activity against Baf3-EGFRL858R/T790M/C797S and Baf3-EGFRDel19/T790M/C797S cancer cell lines with IC50 values in the nanomolar range. Among them, compound Y9m showed the most potent inhibitory activity with IC50 values as low as 8-9 nM. Mechanistic studies showed that Y9m effectively inhibited EGFR L858R/T790M/C797S and EGFRDel19/T790M/C797S kinases, which modulate the phosphorylation of the EGFR signaling pathway proteins. Notably, PI3K phosphorylation in the mTOR signaling pathway decreased as compound concentration increased, which implies that Y9m enhances anti-tumor activity by blocking the phosphorylation of the dual signaling pathways. Y9m induced cell cycle arrest at the G0/G1 phase by inducing apoptosis through the inhibition of CyclinD1 expression and regulating Caspase-3 expression. In conclusion, Y9m is a promising candidate in the development of highly efficacious anticancer agents.