In modern shipping logistics, multi-objective ship route planning has attracted considerable attention in both academia and industry, with a primary focus on energy conservation and emission reduction. The core challenges in this field involve determining the optimal route and sailing speed for a given voyage under complex and variable meteorological and oceanographic conditions. Typically, the objectives revolve around optimizing fuel consumption, carbon emissions, duration time, energy efficiency, and other relevant factors. However, in the multi-objective route planning problem involving variable routes and speeds, the extensive solution space contains a substantial number of unevenly distributed feasible samples. Traditional heuristic optimization techniques, such as multi-objective evolutionary algorithms, which serve as the core component of optimization programs, suffer from inefficiencies in exploring the solution space. Consequently, these algorithms may tend to converge toward local optima during population iteration, resulting in a solution set characterized by sub-optimal convergence and limited diversity. This ultimately undermines the potential benefits of routing optimization. To address such challenging problem in route planning tasks, we propose a self-adaptive intelligent learning network aiming at capturing the potential evolutionary characteristics during population iteration, in order to achieve high-efficiency directed optimization of individuals. Additionally, an uncertainty-driven module is developed by incorporating ensemble forecasts of meteorological and oceanographic variables to form the Pareto frontier with more reliable solutions. Finally, the overall framework of the proposed learning-based multi-objective evolutionary algorithm is meticulously designed and validated through comprehensive analyses. Optimization results demonstrate its superiority in generating routing plans that effectively minimize costs, reduce emissions, and mitigate risks.