The effects of ester addition on structural and dynamic properties of biodegradable ILs composed of the 1-(alkoxycarbonyl)-3-alkylimidazolium cation ([C(1)COOC(n)C(1)im](+), n = 1, 2, 4) coupled with [Br](-), [NO3](-), [BF4](-), [PF6](-), [TfO](-), and [Tf2N](-) are explored using the molecular dynamics (MD) simulations and quantum theory of atoms in molecules (QTAIM) at 400 K. Formation of the intramolecular H bonds between O atoms of the ester group and H atoms of the imidazolium ring as well as the nearest H atom of the alkyl chain to the ester group are disclosed from reduced density gradient (RDG) results. Nano-scale organization that leads to aggregation of the alkyl chain into the uncharged domains and formation of different morphologies can be dearly found by the results of site-site static partial structure factors of cations. Despite the fact that H atoms of the imidazolium ring are more acidic than the nearest H atoms of the alkyl side chain to the ester group, the cation-cation spatial distribution functions (SDFs) and the velocity SDFs demonstrate a reverse trend. This corresponds to the long-range organization of cations and nanoscale arrangement. Transport properties were calculated using the Green-Kubo and Einstein relations. Cations totally diffuse faster than anions and their discrepancies gradually vanish with elongation of the alkyl side chain. The translational motion of the terminal carbon atoms of the ester-functionalized cations decrease when the alkyl group is elongated, whereas the reverse trend is reported for common imidazolium-based ILs. The dynamic heterogeneity of selected ILs is comprehensively investigated by the computing vibrational density of states, van Hove function, and non-Gaussian parameter. Non-Gaussian parameters are finite over the entire time scale for ILs composed of bulkier cations and diverge from zero, verifying the long-lived cage effect. Nanoscale ordering is believed to be responsible for these observations. Finally, the simulated viscosity and ionic conductivity are in good agreement with the experimental data.