Determination of melt rheological behavior within micro-structured geometry is very important for the accurate simulation modeling of micro-molding. Yet studies on the rheological behavior of polymer melts, flowing through micro channels, are complicated due to a large number of factors affecting the melt viscosity. One factor, viscous dissipation, is investigated in the current work through a novel experimental technique to determine the viscous dissipation of a polymer melt flowing through several micro channels with identical aspect ratio. Relative tests are conducted with the melt of high density polyethylene (HDPE) at different temperatures being extruded through the capillary dies with diameters $1000{mu}m$, $500{mu}m$ and $350{mu}m$, respectively. It was found that the temperature rise due to viscous dissipation decreases significantly with the reduction of the characteristic size of micro channel at the same shear rate. In addition, based on the suggested model of radial temperature distribution, the influence of viscous heating on the melt viscosity is investigated. The results indicate that viscous dissipation does not play a significant role.