Phospholipid quantum dot (QD) micelles have been extensively used as fluorescent tags in single nanoparticle imaging for biomedical imaging. In this work, the microscopic structures and photophysical properties of the phospholipid QD micelles were studied at the single nanoparticle level. Two commonly used types of phospholipid QD micelles were prepared and tested both on a solid-phase surface and in liquid phase, including 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-encapsulated QD micelles (DSPE-QDMs) and 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy- (polyethylene glycol)-2000]-encapsulated QD micelles (PEG-DSPE-OPMs). Their fluorescence intensities and diffusion trajectories were determined by a total internal reflection fluorescence-based single nanoparticle imaging platform and comparatively analyzed carefully. It was demonstrated that DSPE-QDMs possessed a comparably wider intensity distribution and lower diffusion coefficient than that of PEG-DSPE-QDMs. PEG-DSPE-QDMs exhibited an obvious fluorescent intenmittence. The results suggested that for most of the DSPE-QDMs, more than one QD were encapsulated in a single micelle. On the other hand, only one QD was embedded in a single micelle of PEG-DSPE-QDMs for most of the cases. Such variances suggested that phospholipids play a key role in the fabrication of the QD micelles. This work provides a useful foundation for their further biomedical applications.