Flavins are widely present in organisms and active centers of many electron-transfer reactions. Therefore, they play an important role in biological electron transport chains. Electron transfer caused by light excitation of flavins is the initial step of many living processes. Cryptochromes containing flavin as a cofactor undergo a series of electron-transfer steps to form spin-correlated radical pairs (SCRP) after light excitation. Cryptochromes are considered the most likely candidate for an avian magnetoreceptor, which initiated research on the dynamics of the electron transfer in the flavin system, especially on their spin dynamics. The study of electron transfer and related processes in flavoproteins will allow one to understand biochemical mechanisms and reveal the influencing factors of various living processes. Therefore, numerous research methods, including UV-Vis spectroscopy, fluorescence spectroscopy, transient absorption spectroscopy, electron paramagnetic resonance, photochemical induced dynamic nuclear polarization (photo-CIDNP) and other spectroscopic techniques. We review studies of domestic and foreign scholars on electron transfer of flavin systems, and discuss the recent progress in various major research methods. UV-Vis spectroscopy is mainly used to study electronic excitation, spin-dynamics, and electron transfer in the flavin systems. UV-Vis spectroscopy might identify the groups involved in electron transfer and perform quantitative analysis combined with theoretical predictions. Fluorescence spectroscopy can identify electronically excited species, observe the rise and decay of, for example, flavin and semiquinone intermediates during the reaction course, and identify their redox and protonation states. Transient optical spectroscopy is suitable for capturing short-lived species that appear in the reaction process. In particular, introducing femtosecond pump-probe technology greatly shortened the time-resolution of observation and can distinguish between singlet- and triplet-born radical pair dynamics. Photo-CIDNP nuclear magnetic resonance (NMR) allows -to observe the electron-nuclear spin dynamics directly. Such direct access to the bio-geomagnetic operational mechanism might pave the way for practical applications. Magnetic field-dependent photo-CIDNP NMR reveals the factors controlling the singlet-to-triplet interconversion and suggests a possible chemical mechanism of bio-geomagnetic navigation. The application of cavity absorption and single-molecule spectroscopy technically improves the sensitivity of the experimental device and reduces the detection limit. This article mainly introduces the various spectroscopic techniques to study the electron-transfer process of flavin systems and their research results. Finally, possible future developments in this field are briefly discussed.