3D printing technique offers lightweight, compact and flexible thermal components that can be integrated into bendable and curved form factors. However, their low thermal conductivity of the polymer‐based backbone structures degrades thermal performances, thereby demanding the rational solution to compensate heat transfer rates. Herein, we report a thermally functional coating of multi‐walled carbon nanotubes (MWCNT) and polyethyleneimine (PEI) through a layer‐by‐layer (LbL) deposition process for a 3D‐printed polymer heat sink (3DP‐HS). The 3DP‐HS is manufactured using the fused filament fabrication and can withstand bending and twisting while solution‐processed LbL self‐assembly directly deposits ultra‐thin MWCNT‐PEI bilayers through stacking materials dissolved in positively and negatively charged solutions using electrostatic attraction. Comparing with the flat polymer plate, the 3DP‐HS validates the heat dissipation function, confirmed via the improved heat transfer coefficient (HTC). Furthermore, the LbL MWCNT‐PEI bilayers highly increase the enhancement rate over 85% owing to extended nanoporous areas and air‐flow mixing on the rough surface. Precise analyses of thermal performances for 10 and 30 MWCNT‐PEI bilayers (∽120–180 nm in thickness) elucidate the proper LbL surfaces on HS, in accordance with heat generation levels. This work would lead to developing a facile yet effective functional coating process for various 3D‐printed thermal management components.This article is protected by copyright. All rights reserved.