In this letter, detection of target protein molecules has been demonstrated by a two-dimensional (2D) photon burst analysis technique and microfluidic channel device. Individual molecule events are scatter plotted in terms of their photon counts and burst width in 2D photon burst analysis. Detection of target protein is verified by a higher counts-per-bin for rabbit anti-HA polyclonal antibody sample than that of the control sample from the 2D photon burst analysis. Since this is microfluidic single molecule detection scheme, it has the advantages of high sensitivity, small sample consumption and reduced processing time, comparing to the conventional immunological ensemble measurements, such as western blot, immuno-precipitation, etc.