A detailed understanding of the photochemical and photophysical properties of individual quantum dots (QD) and QD-dye nanoassemblies upon temperature lowering is essential for understanding the physics of quantum-confined nanoassemblies as well as for their future applications. This chapter discusses temperature-dependent exciton–phonon coupling in Cadmium selenide (CdSe)/ZnS QDs capped by trioctylphosphine oxide ligands and embedded into a glass-forming liquid. It investigates the interplay of phonons in the CdSe core and ZnS shell and the relation to specific excitonic states of the QD. One long-standing question in QD physics is the effect of quantum confinement on the strength of exciton–phonon coupling and phonon frequency, a topic that has received considerable experimental and theoretical attention. The strength of exciton–phonon coupling bears relevance to several fundamental issues of nanoscale physics: exciton relaxation dynamics, homogeneous line widths, and electronic structure. Exciton–phonon coupling has also been investigated for CdSe/ZnS QDs capped by long-chain amines.