Extraordinary optical transmission (EOT) has attracted increasing attention from researchers around the world since its discovery in 1998. In attempt to interpret this abnormal phenomenon caused by nano-hole array structures, the majority of academia take the theory of surface plasmon resonance as the main reason, though minors resort to other theories. Nevertheless, significant amount of research has revealed the factors that are associated with EOT spectra. In particular, the association of molecules with the surface of the nano-hole array can be linearly related to the red-shifted change of EOT spectrum, lending EOT based nano-hole array a unique capability of detecting biochemical events. Such biochemical analysis is label-free, real-time, highly sensitive, promising great potentials in miniaturization of EOT-based advanced instrument. By summarizing the research progress, achievements, and trends of EOT, including its theory and application in biochemical analysis, this paper aims to provide reasonably-deep insights into this exciting area. To this end, EOT is firstly briefly introduced, followed by its physical mechanism and effects. Then recent advances in EOT-based biochemical analysis is presented, with a focus on three representative research teams. Finally, an outlook on the EOT-based biochemical analysis is given.