An improved design of raccoon microchannel heat sink with a combined change in wave amplitude and wavelength along the channel length is proposed in this work. A three-dimensional conjugate heat transfer model studies the characteristics of fluid flow and heat transfer numerically. The total channel length is divided into three zones of equal length where the channel expansion factor (α) and waviness (γ) are varied in each zone to create six sets of modified raccoon microchannels (MRMC). The results indicate that changing the waviness (γ) along an equally divided length of the channel in MRMC contributed to disturbance of the core fluid region and intensified the mixing of laminar boundary layer that enhances the thermal performance of the microchannel. The assessment of MRMC is based on the thermal performance factor (η), and the results indicate that there exists an optimal combination of wave amplitude and wavelength arrangement along the channel length, which has an additive effect on the thermal performance. The Nusselt number and friction factor of the new heat-sink design is well demonstrated by comparison with the simple raccoon microchannel (SRMC). In addition, a wide range of parametric variations is also considered to indicate the axial wall conduction effect in raccoon microchannels. © 2019 by Begell House, Inc.