The structural and dynamical properties of two cholinium-based naphthenic acid ionic liquids (CBNALLs), namely, cholinium cyclopentane carboxylate aCHHCPCD and cholinium cyclohexane carboxylate ([CH][CHC]) have been studied using the classical molecular dynamics simulations and quantum mechanical methods. The results have also been compared with corresponding aromatic ones. Interaction energies, charge transfers, and hydrogen bondings between the studied ion pairs were investigated by density functional theory calculations and also the theory of atoms in molecules. Density, mean-square displacement, self-diffusivity, viscosity, electrical conductivity, transference number, ionicity, and fragility have been computed for the studied CBNAILs in the temperature range of 298.15-450 K and at 0.1 MPa. The simulated values were in good agreement with experimental data where they exist. The structural features of these CBNAILs were characterized by calculating the partial site site radial distribution functions and spatial distribution functions. The results show a density cap of hydrogen atoms of hydroxyl groups of cations extended along the COO groups of anions. In these ILs, [CPC](-) and [CHC] are connected by hydrogen bonding to [CH](+) mainly through the carboxylate group. Increasing the number of carbon atoms in the ring of [CHC](-)-with respect to [CPC] makes remarkable changes in self-diffusions, electrical conductivities, and viscosities. Altogether, this work gives a better insight into the dynamics and structuring of this class of biodegradable ILs at a molecular level.