The introduction of blockchain technology provides an effective solution to the problems in shipping logistics such as low transparency and low efficiency of transportation documents. However, the construction of blockchain system led by different members of shipping chain can have different effects on the operational decisions of all parties. In this regard, by taking into account shippers’ preference for traceability information, a three-level shipping supply chain composed of ports, carriers and freight forwarders is constructed, where each party leads the construction of the blockchain traceability system. On the basis of cost sharing strategy, the Stackelberg game model is used to compare and analyze the optimal pricing strategy under the benchmark model and the three blockchain technology models. In addition, the subsidy intensity and members’ pricing strategies under different government subsidy models are considered. The research results show that blockchain technology is not always the optimal decision-making for members of the shipping supply chain, but is related to the cost-sharing ratio, shippers’ preference for traceability information, and the delay cost of shipping documents. When shippers’ preference for traceability information is high but the cost of traceability is low, all parties should improve the traceability to increase respective revenue. Although the government’s fixed subsidy model cannot bring benefits to followers, while in the retrospective subsidy model, when the sharing ratio of the leaders of the shipping chain is higher than a certain threshold, the enhanced traceability subsidy intensity will bring maximum profits to the entire supply chain.