Special vehicles named flat transporters are used to deliver heavy ship assembly blocks in shipyards. Because each movement of assembly blocks among workshops needs transporters and the transportations are time-consuming, the scheduling of transporters is important for maintaining the overall production schedule of assembly blocks. This paper considers an optimization transporter scheduling problem for assembly blocks. The objective is to minimize logistics time, which includes empty travel time of transporters and waiting time and delay time of block tasks. Considering time windows of ship blocks, carrying capacity of transporters, and precedence relationships of tasks, a mathematical model is proposed. A hybrid topological graph is used to denote precedence and cooperating relationships of tasks. A metaheuristic algorithm based on the hybrid topological graph and genetic algorithm and Tabu search is proposed. The performance of the algorithm was evaluated by comparing the algorithm to optimal result in small-sized instances and several strategies in large-sized instances. The results showed the efficiency and effectiveness of the proposed algorithm.