In this study, a carbon nanotube-glass bubble/polyamide 6 (CNT-GB/PA6) multiscale hybrid composite was manufactured. Through a coagulation process including CNT and GB, a segregated network was formed to produce a composite structure with tunable thermal conductivity. Within the segregated network structure, a complex phenomenon of decrease and increase in thermal conductivity owing to the interaction by CNT and GB, and an equation to predict thermal conductivity through the contents of GB and CNT was formulated. A model to predict the thermal conductivity using the RSM analysis was presented, and the contents of GB and CNT were adjusted according to the required thermal conductivity. It was confirmed through the LFA thermal conductivity measurement that the thermal conductivity increased with GB and CNT contents. Moreover, when 30% of GB was added to the 5 wt% CNT composite, the thermal conductivity increased by about 17%. However, in the experiment to confirm the effect of GB alone, it was confirmed that the thermal conductivity decreased as the GB content increased. Thus, the size of the structural path, which was controlled by the GB content through which electrons pass, played an important role in this study. The results of this study can be used in astronautic fields that require insulation to save energy and in construction engineering where thermal insulation and heat emission are important.