In the context of digital transformation in the shipping industry, the divergent overbooking behaviors of liner companies in both online and offline channels have altered the supply-demand matching relationship in each channel. This results in heterogeneous cost structures, which further complicates the slot allocation in dual-channel. To address this challenge, this paper categorizes shippers into freight rate-sensitive and freight rate-insensitive types and then develops a joint optimization model for dual-channel slot allocation and pricing. Furthermore, empty container repositioning is incorporated into the decision-making framework, and a two-stage nonlinear programming model is established to synchronously optimize slot allocation quantity, freight rates, and empty container repositioning volume. A shipping route from the Far East to South Africa operated by COSCO Shipping is selected as a case study for numerical and sensitivity analyses. Results show that compared with the mode that ignores empty container repositioning, considering this factor can increase the liner company’s expected total profit by 32%. In addition, when parameters such as the fulfillment rate of shippers in the spot market, the confidence level of shippers in the contract market, and the random demand fluctuation in the spot market change, the mode considering empty container repositioning exhibits better profit stability. By the refined classification of shipper types, this paper provides theoretical support and decision-making reference for the operational management of liner companies in the context of shipping digitalization.