The composition and carbon nanostructure of soot are important parameters influencing health and climate effects, and the efficacy of soot mitigation technologies. We used laser-vaporization, electron-ionization aerosol mass spectrometry (or SP-AMS) to systematically investigate relationships between aerosol mass spectra, carbon nanostructure (HRTEM), and composition (thermal-optical carbon analysis) for soot with varying physicochemical properties. SP-AMS refractory black carbon concentrations (based on clusters) were correlated to elemental carbon (r = 0.98, p < 10−8) and equivalent black carbon (aethalometer) concentrations. The SP-AMS large carbon (C+≥6, midcarbons and fullerene carbons) fraction was inversely correlated to fringe length (r = −0.97, p = 0.028) and linearly correlated to the fraction of refractory organic carbon that partially pyrolize during heating (r = 0.89, p < 10−4). This refractory organic carbon material was incompletely detected with conventional aerosol mass spectrometry (flash vaporization at 600 °C). This suggests that (SP-AMS) refractory carbon cluster analysis provides insight to chemical bonding and nanostructures in refractory carbon materials, lowcarbons (C+≥5) indicate mature soot and large carbons indicate refractory organic carbon and amorphous nanostructures related to C5-components. These results have implications for assessments of soot particle mixing state and brown carbon absorption in the atmosphere and enable novel, on-line analysis of engineered carbon nanomaterials and soot characteristics relevant for climate and health.