This article contains the data set and model code for the negative emission polygeneration system described in Tan et al. (2019). The data was generated utilizing an optimization model implemented in LINGO 18.0 and includes information on the operating state of each process unit in the system. The maximum annual profit of the system was determined at different carbon footprint targets. The data set and model code can be utilized for further analysis on the interdependence between the process units of this polygeneration system, its operational and environmental performance, and the potential impact of integrating new process units into the network.