Small molecules (biological small molecules) in vivo are not only in a large number, involving inorganic small molecules, such as SO 2 , H 2 S, NO and CO, and more organic small molecules, such as monosaccharides, oligosaccharides, hormones, coenzymes, glycerol, stimulating factors, regulatory factors, Vitamins, etc., moreover, play an important role in pathology, physiology, and so on. Therefore, it is necessary to observe and monitor small molecules in vivo in real time, and the two-photon fluorescence probe is a necessary tool to achieve this goal. The advantages of two-photon fluorescence probe, such as fixed target (very small dot) excitation, high horizontal and vertical resolution, no photobleaching, no phototoxicity and deep imaging in tissues, and so on, demonstrate its unparalleled superiority. It can be used for dynamic 3D observation and monitoring of biological small molecules in cells or tissues. In this paper, CO, monosaccharide (glucose, β-galactosidase), SO 2 , H 2 S, NO, peroxy (sulfur) compounds, mercaptan/thiophenol, 1 O 2 , formaldehyde, HNO, HclO, O 2 •− and ONOO − two-photon fluorescence probes which have been developed in recent 5 years were reviewed. The sensing mechanisms of these two-photon fluorescence probes were systematically analyzed, and the development and prospect of two-photon fluorescence probes for small biomolecules are prospected.