It is crucial to design multi-functional structure to improve heat transfer characteristics. Here we report significantly enhanced saturated flow boiling heat transfer of water using the two-tier vertically aligned multiwalled carbon nanotube (VAMWNT) channel (tube diameter: 11.5 nm). The channel size is 10 × 10 × 2 mm3 (height: 2 mm). The tube aggregation-generated large voids act as micropores (10-200 µm) whereas the interstitial spaces between the tubes act as nanopores (< 72 nm). The microcavities at the periphery of aggregated nanotubes increase bubble nucleation sites while constraining bubble size. The high nanotube thermal conductivity induces more uniform bubble nucleation, and departed bubbles are swept away through the micropores. On the other hand, water is effectively replenished through the nanopores by high capillary pumping. Overall, the path separation of bubble departure and water replenish effectively prevents dryout and increases critical heat flux (CHF). The experiment is carried out at 3 different mass velocities (62, 83, and 104 kg m−2 s−1). The VAMWNT channel provides a high heat transfer coefficient (h = 100,666 W m−2 K−1 at 183 W cm−2), even before reaching CHF without any sign of local dryout, compared with microchannels and porous media in literature (under the similar heat flux and mass velocity). In contrast, the CHF condition is observed for a plain channel of the same size without the nanotubes, resulting in smaller h values than those of the VAMWNT channel. The novel two-tier structure separated liquid-vapor pathways, significantly enhancing heat transfer characteristics.