Multi-fidelity modeling (MFM) is an evolving field that matches low-fidelity models (LFM) and high-fidelity models (HFM) to get better solutions with low computational cost. However, improving the duality between accuracy and computational cost remain challenging, particularly for complex problems such as dual fuel engines. This paper contributes to the MF modeling cost-effectiveness improvement by proposing a new approach to solve large-dimensional multi-objective optimization problems. The first step is to build a meta-model based on the LF model, which will be subjected to a comet-governed analysis to detect potential areas where the uncertainty on the LF model is relatively high. Then, a design of experiment (DOE) will be developed based on the results of this analysis to construct an initial HF model. Finally, an iterative loop will be activated to improve the accuracy of the MF model using a well-weighed combination of the details delivered by the LF model correction via the HF model and the HF meta-model. The developed approach is validated on four different mathematical benchmarks with different difficulties, compared with four different MF modeling strategies. This validation shows that the proposed MF modeling is competitive and can produce solutions as accurate as the HF model while reducing significantly the overall computation time by up to 50%. As an engineering application, the operating conditions in a natural gas-hydrogen/diesel dual fuel engine in terms of compression ratio, pilot injection timing, and EGR are optimized. A reduction of 46%, 68%, and 96% was achieved for HC, NOx, and the knocking index, respectively, while an increase in thermal efficiency of about 5% was obtained.