Due to confined space in micro heat pipes (MHPs), the resulting flow boiling heat transfer suffers from flow instability and low values of critical heat flux. In this paper, to overcome this challenge, different shapes of silicon and copper micro pillars were designed inside the micro axial grooves of silicon-based MHPs and fabricated by MEMS fabrication methods. The capillary rise test and thermal performance test were performed to investigate the wettability and effective thermal conductivity of MHPs. The results showed the performance of MHPs with circular micro pillar was superior to square and diamond shapes. In addition, the hydrophilicy and thermal performance of copper micro pillars were more effective than silicon micro pillars. Comparative study of micro pillars with straight and zigzag patterns showed that the capillary and thermal performance of zigzag pattern was preferable to straight one. In this case, contact angles of Wenzel model for straight and zigzag patterns achieved 24.38° and 18.49°, respectively. Our findings illustrated the micro pillars not only improved the wettability of micro grooves but also increased the heat transfer capability of two-phase flow inside the MHPs.