Aquathermolysis is one of the crucial processes being considered to successfully upgrade and irreversibly reduce the high viscosity of heavy crude oil during steam enhanced oil recovery technologies. The aquathermolysis of heavy oil can be promoted by transition metal-based catalysts. In this study, the catalytic performance of two water-soluble catalysts Ni(CH3COO)2 and Zn(CH3COO)2 on the aquathermolytic upgrading of heavy oil at 300 °C for 24 h was investigated in a high pressure–high temperature (HP-HT) batch reactor. The comparison study showed that nickel acetate is more effective than zinc acetate in terms of viscosity reduction at 20 °C (58% versus 48%). The viscosity alteration can be mainly explained by the changes in the group composition, where the content of resins and asphaltenes in the upgraded heavy crude oil sample in the presence of nickel catalyst was reduced by 44% and 13%, respectively. Moreover, the nickel acetate-assisted aquathermolysis of heavy oil contributed to the increase in the yield of gasoline and diesel oil fractions by 33% and 29%, respectively. The activity of the compared metal acetates in hydrogenation of the crude oil was judged by the results of the atomic H/C ratio. The atomic H/C ratio of crude oil upgraded in the presence of Ni(CH3COO)2 was significantly increased from 1.52 to 2.02. In addition, the catalyst contributed to the desulfurization of crude oil, reducing the content of sulfur in crude oil from 5.55 wt% to 4.51 wt% The destructive hydrogenation of resins and asphaltenes was supported by the results of gas chromatography-mass spectroscopy (GC-MS) and Fourier-transform infrared (FT-IR) spectroscopy analysis methods. The obtained experimental results showed that using water-soluble catalysts is effective in promoting the aquathermolytic reactions of heavy oil and has a great potential for industrial-scale applications.