The control of heat transport in organic materials has attracted increasing attention for developing thermal transistors and other heat-regulating devices. Here, we demonstrate continuous and reversible modulation of the thermal conductivity ( \({\kappa }_{\perp }\) ) of polymer poly[2,5-bis(3-alkylthiophen-2-yl)thieno[3,2-b]thiophene] (PBTTT) films along the lamellar-stacking (out-of-plane) direction via electrochemical doping. \({\kappa }_{\perp }\) values were quantitatively evaluated under gating conditions using a gold-based time-domain thermoreflectance system. Upon electrochemical doping, \({\kappa }_{\perp }\) increased by 28%, from 0.198 to 0.253 W m−1 K−1, and the modulation of the thermal conductivity by the shift of gate voltage is achieved. Atomistic simulations revealed how molecular intercalation and the associated changes in local structural conformation affect spectral thermal transport in the host PBTTT matrix, providing insight into the mechanism behind the increased \({\kappa }_{\perp }\) . These results confirm that electrochemical doping enables reversible and controllable tuning of thermal conductivity, a key requirement for thermal management applications, paving the way for future advancements in thermally tunable organic materials.