Shuttle bus connection is a valid technique to handle unplanned problems and promote sustainable transportation. The study describes tools that facilitate the shuttle bus timetable adjustment responding to a disturbance resulting from behind-schedule trains on a commuter railway. This behind-schedule disturbance is divided in four stages allowing for different delay ranges. The problem and its solution involve different elements, such as shuttle bus route selection, stop location, and timetable adjustment. We propose a nonlinear integer programming model, in which the objective function is based on the waiting, travelling, and walking costs for passengers as well as the operation cost of the route chosen. Vehicle capacity constraints and precise passengers’ waiting times are considered. A genetic algorithm and a simulated annealing algorithm combined with a priori decomposition are used to derive an efficient solution. A case study of a shuttle bus serving the Jinshan Railway in Shanghai, China, is tested to validate that, compared to the no-planning timetable, the total cost of the optimized timetable is reduced by 7.6%, especially including a dramatic reduction in the cost of passenger waiting time by 49.1%.