We employ photoluminescence (PL) spectroscopy on individual nanoscale aggregates of the conjugated polymer poly(3-hexylthiophene), P3HT, at room temperature (RT) and at low temperature (LT) (1.5 K), to unravel different levels of structural and electronic disorder within P3HT nanoparticles. The aggregates are prepared by self-assembly of the block copolymer P3HT-block-poly(ethylene glycol) (P3HT-b-PEG) into micelles, with the P3HT aggregates constituting the micelles' core. Irrespective of temperature, we find from the intensity ratio between the 0-1 and 0-0 peaks in the PL spectra that the P3HT aggregates are of H-type nature, as expected from π-stacked conjugated thiophene backbones. Moreover, the distributions of the PL peak ratios demonstrate a large variation of disorder between micelles (inter-aggregate disorder) and within individual aggregates (intra-aggregate disorder). Upon cooling from RT to LT, the PL spectra red-shift by 550 cm-1, and the energy of the (effective) carbon-bond stretch mode is reduced by 100 cm-1. These spectral changes indicate that the P3HT backbone in the P3HT-b-PEG copolymer does not fully planarize before aggregation at RT and that upon cooling, partial planarization occurs. This intra-chain torsional disorder is ultimately responsible for the intra- and inter-aggregate disorder. These findings are supported by temperature-dependent absorption spectra on thin P3HT films. The interplay between intra-chain, intra-aggregate, and inter-aggregate disorder is key for the bulk photophysical properties of nanoparticles based on conjugated polymers, for example, in hierarchical (super-) structures. Ultimately, these properties determine the usefulness of such structures in hybrid organic-inorganic materials, for example, in (bio-)sensing and optoelectronics applications.