In order to give full play to the competitive advantages of the ports in Guangdong-Hong Kong-Macao Greater Bay Area and promote the coordinated of port economy, this paper constructed a supply chain game model and carried out numerical simulation to study the impact of relevant factors on the performance of Shenzhen port and Hong Kong port, based on the actual situation of the main ports in Guangdong-Hong Kong-Macao Greater Bay Area. The results showed that with the increase of commodity price and inventory cost, goods were transferred from Shenzhen port to Hong Kong port, but the transfer range gradually slowed down. Shenzhen port had obvious competitive advantages in the supply collection of medium and low-end goods, while Hong Kong port was more attractive to high-end goods. The gradual transition of freight structure to medium and high-end commodities could promote the improvement of port revenue. Among them, Shenzhen port should reduce the operation risk by reducing the cost of commodity inventory. The opening of the Shenzhen-Zhongshan channel and the Hong Kong-Zhuhai-Macao Bridge would effectively shorten the transportation time in the hinterland, and would increase the total revenue of the ports in Guangdong-Hong Kong-Macao Greater Bay Area for most of the combination of commodity prices and inventory costs.