The flow field in a channel with staggered pin-fin array was measured using time-resolved Particle Imaging Velocimetry (PIV). The distributions of flow field statistics were compared with that of Nusselt number on the end wall measured by thermochromic liquid crystal (TLC) of the same geometry. Lower order large-scale fluctuation and higher order small-scale disturbances were examined separately using Proper Orthogonal Decomposition (POD) to study the flow field characteristics and their individual effect on the heat transfer enhancement. Pin fins with circular and square cross-section geometries were studied at Reynolds numbers of 10000 and 20000. Results indicate that for circular pin fins, the distribution of lateral/transverse velocity fluctuations or turbulent kinetic energy from large scale vortex shedding resembles that of local Nu, and the heat transfer augmentation downstream of the recirculation zone is dominant, while the heat transfer enhancement is limited in the shear layer on both sides of recirculation where disturbances are small-scale. However, for square pin fins, heat transfer augmentation in the shear layer is as strong as that downstream of recirculation, while large scale fluctuations downstream is much weaker than small scale disturbances in the shear layer. Compared to small scale disturbances, large scale fluctuations are found to contribute more efficiently to end wall heat transfer enhancement both for circular and square pin fins. Large scale fluctuation, as well as heat transfer enhancement weakens with the increase of Reynolds number, while smaller scale disturbance grows stronger at the same time.