An apparatus and a method for measuring blood flow of vessels are provided. A light source, a light splitting module, a reference arm module, a sample arm module, a probing module, and a control system are arranged； the sample arm module includes a scanning unit and an optical-path shifting device； a probe light is obtained from the light splitting module, and a main light of the probe light is on a rotating shaft of the scanning unit； the probe light is reflected by the scanning unit to the optical-path shifting device, when the optical-path shifting device is in a first position and in a second position respectively, the probe light scans a vessel in fundus to obtain a first phase shift signal and a second phase shift signal blood flow rates and total blood flow of all the vessels near an optic disc are determined.
