Acute kidney injury (AKI) is a clinically common and severe disease with a significant economic burden worldwide. Although several studies have focused on the pathogenesis of AKI, much remains unknown about its complex molecular regulatory network and pathophysiological mechanisms. This study combines mass spectrometry and RNA sequencing technologies to investigate nephrotoxin-induced AKI mice's protein and RNA expression profiles. The results revealed that Slc34a1 and Slc34a3 were significantly down-regulated in nephrotoxin-induced AKI mice and may be potential diagnostic and therapeutic targets.