We study the temperature dependence of time-resolved photoluminescence (PL) in closely packed alignment of Si nanodisks (NDs) with SiC barriers, fabricated by neutral beam etching using bio-nano-templates. The PL time profile indicates three decaying components with different decay times. The PL intensities in the two slower decaying components depend strongly on temperature. These temperature dependences of the PL intensity can be quantitatively explained by a three-level model with thermal activation energies of 410 and 490 meV, depending on the PL components. The activation energies explain PL quenching due to thermal escape of electrons from individual NDs. This thermal escape affects the PL decay times above 250 K. Dark states of photo-excited carriers originating from the separate localization of electron and hole into different NDs are elucidated with the localization energies of 70 and 90 meV. In contrast, the dynamics of the fastest PL decaying component is dominated by electron tunneling among NDs, where the PL intensity and decay time are constant for temperature.