The development of fluorophores for the second near-infrared window (NIR-II, 1000-1700 nm) represents an emerging, significant, and vibrant field in analytic chemistry, chemical biology, and biomedical engineering. The wavelength, brightness, and stability are three crucial factors that determine the performance of an NIR-II fluorophore. Up to now, significant progress has been made in the development of NIR-II fluorescence molecular probes, including the synthesis of D-A-D and D-π-A fluorophores with improved NIR-II fluorescence imaging performance and the construction of off-on probes and ratiometric probes via energy transfer or molecular structure modification. In this review, we summarize the most recent advances in molecular engineering design strategies of NIR-II fluorophores and probes, then highlight a selection of bioimaging and biosensing applications. We also provide perspectives on potential challenges and opportunities in this emerging field.