In this paper, we propose a new ship scheduling set packing model considering limited risk or variance. The set packing model is used in many applications, such as vehicle routing, crew scheduling, ship scheduling, cutting stock and so on. As long as the ship scheduling is concerned, there exits many unknown external factors such as machine breakdown, climate change and transportation cost fluctuation. However, existing ship scheduling models have not considered those factors apparently. We use a quadratic set packing model to limit the variance of expected cost of ship scheduling problems under stochastic spot rates. Set problems are NP-complete, and additional quadratic constraint makes the problems much harder. We implement Kelley's cutting plane method to replace the hard quadratic constraint by many linear constrains and use branch-and-bound algorithm to get the optimal integral solution. Some meaningful computational results and comments are provided.