Abstract: Most heavy crude oils underwent biodegradation and generated a significant amount of naphthenic acids. Naphthenic acids are polar compounds with the carboxylic group and are considered as a major factor affecting the oil viscosity. However, the relationship between the molecular composition of naphthenic acids and oil viscosity is not well understood. This study examined a “clean” heavy oil with low contents of heteroatoms but had a high content of naphthenic acids. Naphthenic acids were fractionated by distillation and caustic extraction. The molecular composition was characterized by high-resolution Orbitrap mass spectrometry. It was found that the 2- and 3-ring naphthenic monoacids with 15–35 carbon atoms are dominant components of the acid fractions; the caustic extraction is capable of isolating naphthenic acids with less than 35 carbons, which is equivalent to the upper limit of the distillable components, but not those in the residue fraction; the total acid number of the heavy distillates is higher than that of the residue fraction; the viscosity of the distillation fraction increases exponentially with an increased boiling point of the distillates. Blending experiments indicates that there is a strong correlation between the oil viscosity and acids content, although the acid content is only a few percent of the total oil.