Our previous researches proposed a basic green supply chain network model for considering not only environmental but also economic aspects in order to obtain a large amount of profit and to reduce the amount of carbon dioxide emitted during the transportation process . The model consists of two model components; those are clients and suppliers. The model provided a numerical method to determine suitable prices and delivery times of products through the modification processes of both production schedules by using genetic algorithms and transportation schedules by heuristic rules and the negotiation processes between suppliers and clients by using an auction based method in order to obtain profit considering carbon dioxide emissions reductions in the transportation processes. This paper presents an integrated scheduling method of production and transportation problems in order to further reduce carbon dioxide emissions without decreasing profits of suppliers. This method makes an efficient transportation schedule that ensures a low vacancy rate and a high loading rate of transportation vehicles by repeating the modification processes of production and transportation schedules alternately. A prototype of supply chain simulation system is developed for production and transportation scheduling problems. Experiments are carried out on a two-layered supply chain model in order to verify the effectiveness of the proposed method from the viewpoint of both the profits of suppliers and the amount of carbon dioxide emitted from transportation process.