The daisy chain is one of the main layout types of the subsea production system in the development of deepwater oil and gas fields. The number of production loops, length of subsea pipelines, and partition of subsea wells are the main concerns in pigging loop design, pipeline laying, and flow assurance, which become important factors for the capital and operating expenditures and the risk management of deepwater fields. This article focuses on the basic optimal partition problem of production loops for subsea wells in the layout of daisy chains. It proposes to find the optimal partition method at the lowest layout cost, where a mathematical model is proposed and its dedicated algorithm is developed. Numerical simulations are conducted to evaluate the validity of the proposed model and the performance of the algorithm. The results show that the model can accurately describe the optimal partition problem of daisy chains in practice, and a mathematical solution to the optimal partition can be obtained by the algorithm programmed in MATLAB, which can provide the engineers a quantitative reference for the layout of daisy chains in engineering.