Performance evaluation of supply chain (SC) is a vital topic in SC management and inherently complex problems with multilayered internal linkages and activities of multiple entities. Recently, various Network Data Envelopment Analysis (NDEA) models, which opened the “black box” of conventional DEA, were developed and applied to evaluate the complex SC with a multilayer network structure. However, most of them are input or output oriented models which cannot take into consideration the nonproportional changes of inputs and outputs simultaneously. This paper extends the Slack-based measure (SBM) model to a nonradial, nonoriented network model named as U-NSBM with the presence of undesirable outputs in the SC. A numerical example is presented to demonstrate the applicability of the model in quantifying the efficiency and ranking the supply chain performance. By comparing with the CCR and U-SBM models, it is shown that the proposed model has higher distinguishing ability and gives feasible solution in the presence of undesirable outputs. Meanwhile, it provides more insights for decision makers about the source of inefficiency as well as the guidance to improve the SC performance.