The microchannel heat sink is promising heat dissipation method far high density electronic devices. The cross-sectional shape of MEMS based microchannel heat sink is limited to triangular, trapezoidal, and rectangular due to their fabrication method. And heat is added to one side surface of heat source. Therefore, those specific conditions make some complexity of heat transfer in microchannel heat sink. Though many previous research of conjugate heat transfer in microchannel was conducted, most of them did not consider heat loss. In this study, numerical investigation of conjugate heat transfer in rectangular microchannel was conducted. The method of heat loss evaluation was verified numerically. Heat distribution was different for each wall of rectangular microchannel due to thermal conductivity and distance from heat source. However, the ratio of heat from each channel wall was correlated. Therefore, the effective area correction factor could be proposed to evaluate accurate heat flux in one side heating condition.