The flow of lubricant oil films in confined gaps of micro-scale is a significant factor to affect load-carrying capacity of lubrication films in precision machines and micro-electro-mechanical systems (MEMS). In order to research the lubricating property of thin lubricant film the paper established through-thickness velocity profile measurement system and carried out a on-line situ measurement on through-thickness velocity profile of thin oil film under confined micro-gaps, based on fluorescence recovery after photobleaching (FRAP) and imaging analysis of shape changes process in the bleached area. The method adopted an assumption that the fluorescence intensity is distributed and layered along the film thickness direction, combined two-dimensional bleaching ability distribution information varying with time to acquire velocity distribution of the film thickness direction and the velocity profile of a 8 μm thickness of PB450 polybutene lubricant film. Pearson correlation coefficient of the experiment result and reconstructed fluorescent agent intensity distribution curve is greater than 0.95 and the velocity profile conforms to existing lubrication theory, which proves the reliability of the measuring results.