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Nanocarbon aerogels display outstanding electrical and solar-thermal heating efficiencies. However, little is known about the relationship between their microstructure and the heating performance. In this study, two different types of carbon nanotube (CNT) aerogels were synthesized via an ice-templating (IT) and emulsion-templating (ET) approach, respectively, which induces drastic difference in internal microstructures, crosslinking densities and porosities. These structural differences give rise to substantial efficiency differences in electrical aerogel heating (e.g. 46 o C/W for rET-CNT aerogel, 75 o C/W for rIT-CNT aerogel). Systematic comparison of nanocarbon aerogel microstructure in terms of nanocarbon type, envelope density, and nanocarbon graphiticity shows that the Joule-heating efficiency is highly correlated with the thermal conductivities of the aerogels, where aerogels with lower thermal conductivities exhibit higher Joule-heating efficiencies. This relationship is also observed for solar-thermal aerogel heating, with the aerogels of lowest thermal conductivity (rIT-CNT aerogel) exhibiting a 30% higher efficiency in solar water evaporation, compared to rET-CNT aerogels. These results demonstrate that the heating properties of nanocarbon aerogels can be readily tuned and enhanced through structural control alone. The findings provide a new perspective for the design of nanocarbon aerogel for applications that involve electrical or solar-thermal heating, such as temperature-dependent separation, sorption, sensing, and catalysis.