As a crucial path to promote the sustainable development of power systems, shared energy storage (SES) is receiving more and more attention. The SES generates carbon emissions during its manufacturing, usage, and recycling process, the neglect of which will introduce a certain extent of errors to the investment of SES, especially in the context of the large-scale integration of renewable energy and dramatic increase in demand for SES capacity. To enhance the accuracy of SES investment, we propose a double-layer optimization model to compute the optimal configuration of a shared energy storage station (SESS) considering its life-cycle carbon emission. First, the service mode, settlement method, profit mechanism, and application scenarios of SESS are introduced. Second, the life-cycle assessment approach is used to calculate the life-cycle carbon emission of SESS, and the uncertainty of supply and demand is considered. Then, a double-layer optimization model that considers the economic operation of multi-microgrid systems and the optimal allocation of SESS is established. The lower-layer model’s Karush–Kuhn–Tucher (KKT) condition is derived to convert the double-layer model into a single-layer one. Finally, a combined heat and power (CHP) three-microgrid system is used to demonstrate the validity of our proposed model, and the economy of SESS investment is analyzed from multiple perspectives. The results show that considering the life-cycle carbon emission of SESS can provide more accurate guidance for investing in and measuring the carbon emission and reduction for SESS.