The engineered ascorbate peroxidase (APEX) developed by Alice Ting laboratory, compared with classical horse radish peroxidase (HRP), can keep active within all cellular compartments, so it has great potential as a tool for studying the fusion proteins in both subcellular organelles and live cells. Up to now, diaminobenzidine staining based on APEX tag has been successfully developed for electron microscopy (EM) in whole cells, subcellular organelles and proteins. Moreover, combined with mass spectrometry technique, APEX-mediated proximity biotin labeling in living cells greatly promoted the study of subcellular organelle proteomics and temporal-spatial proteomics. This review focused on the principle of APEX methodology, summarized its latest applications including EM imaging and spatial proteomics, and discussed its limitations and challenges as well.