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Wax deposition is one of the major flow problems for petroleum transportation and production. In this context, the development of more efficient methods to remediate paraffin precipitation has received great attention within the oil industries. In the present study, eight new long-chain esters were prepared in less than four synthetic steps and in high yields (84–97%). Seven of them contain naphthoquinone nuclei, and one presents a cyclohexyl group. The new molecules were tested as non-polymer wax precipitation inhibitors and pour point depressants. Calorimetric experiments were employed to identify the effect of four pre-determined chemical groups within the molecules and to set out the best components for maximized inhibition: (i) the length of alkyl chain in the ester group, (ii) the length of the alkyl chain separating the polar nuclei and the ester group, (iii) the heteroatom bonded to the polar nuclei, and (iv) the importance of the naphthoquinone nuclei. After determination of the pour point and wax appearance temperature (WAT) of Brazilian oils by differential scanning calorimetry (DSC), the highest efficiency was observed for naphthoquinone esters derived from stearic and palmitic acids when containing two methylene groups as a separator and nitrogen as the heteroatom. These new additives present better results than the commercially available polymer-based inhibitors in all tested samples, even when applied at smaller concentrations, compared to many other polymer-based inhibitors reported in the literature. The importance of the naphthoquinone moiety as the polar portion of the inhibitor was confirmed when it was replaced by a cyclohexyl group. Molecular modeling and X-ray diffraction studies were also carried out to rationalize the relationship between structure and activity and the action mechanism of these new chemical additives.