We report the use of a sensitive double-clad fiber (DCF) probe for in situ cell flow velocity measurements and cell analysis by means of two-photon excited fluorescence correlation spectroscopy (FCS). We have demonstrated the feasibility to use this fiber probe for in vivo two-photon flow cytometry previously. However, because of the viscosity of blood and the non-uniform flow nature in vivo, it is problematic to use the detected cell numbers to estimate the sampled blood volume. To precisely calibrate the sampled blood volume, it is necessary to conduct real time flow velocity measurement. We propose to use FCS technique to measure the flow velocity. The ability to measure the flow velocities of labeled cells in whole blood has been demonstrated. Our two-photon fluorescence fiber probe has the ability to monitor multiple fluorescent biomarkers simultaneously. We demonstrate that we can distinguish differently labeled cells by their distinct features on the correlation curves. The ability to conduct in situ cell flow analysis using the fiber probe may be useful in disease diagnosis or further comprehension of the circulation system.