［Purposes］To address the sulphur oxides (SO?) and nitrogen oxides (NO?) emission limit requirements in certain sections of shipping routes, a nonlinear programming model is developed with the objective of minimizing the annual total operating cost of the fleet, in which fleet deployment, sailing speed optimization, and emission-reduction measure selection are treated as the key decision variables.［Methods］Based on the above model, an additional emission-reduction option is introduced by considering LNG retrofitting of ships. An improved butterfly optimization algorithm is then employed to solve the model, enhancing solution accuracy and yielding the optimal fleet deployment scheme.［Findings］The research findings can be applied to fleet deployment and sailing speed scheduling decisions for shipping routes that traverse sulphur and nitrogen emission control areas.