To use high-temperature waste heat generated by diesel engines for onboard refrigeration of fishing vessels, an ammonia-based double-effect vapor absorption refrigeration cycle is proposed. Non-volatile ionic liquids are applied as absorbents in the double-effect absorption system. In comparison to systems using ammonia/water fluid, the complexity of the system can be reduced by preventing the use of rectification sections. In this study, a multi-scale method is implemented to study the proposed system, including molecular simulations (the Monte Carlo method) for computing vapor-liquid equilibrium properties at high temperatures and pressures, thermodynamic modeling of the double-effect absorption cycles, and system evaluations by considering practical integration. The Monte Carlo simulations provide reasonable vapor-liquid equilibrium predictions. 1-butyl-3-methylimidazolium tetrafluoroborate is found to be the best performing candidate among the investigated commercialized ionic liquids. In the proposed cycle, the best working fluid achieves a coefficient of performance of 1.1 at a cooling temperature of −5 C, which is slightly higher than that obtained with generator-absorber cycles. Integrated with the exhaust gas from diesel engines, the cooling capacity of the system is sufficient to operate two refrigeration seawater plants for most of the engine operating modes in high-latitude areas. Thereby, the carbon emission of onboard refrigeration of the considered fishing vessel could be reduced by 1633.5 tons per year compared to the current practice. Diagrams of vapor pressures and enthalpies of the studied working fluids are provided as appendices.