Effective management of an urban solid waste system (USWS) is crucial for balancing the tradeoff between economic development and environment protection. A factorial ecological-extended physical input-output model (FE-PIOM) was developed for identifying an optimal urban solid waste path in an USWS. The FE-PIOM integrates physical input-output model (PIOM), ecological network analysis (ENA), and fractional factorial analysis (FFA) into a general framework. The FE-PIOM can analyze waste production flows and ecological relationships among sectors, quantify key factor interactions on USWS performance, and finally provide a sound waste production control path. The FE-PIOM is applied to managing the USWS of Fujian Province in China. The major findings are: (i) waste is mainly generated from primary manufacturing (PM) and advanced manufacturing (AM), accounting for 30% and 38% of the total amount; (ii) AM is the biggest sector that controls the productions of other sectors (weight is from 35% to 50%); (iii) the USWS is mutualistic, where direct consumption coefficients of AM and PM are key factors that have negative effects on solid waste production intensity; (iv) the commodity consumption of AM and PM from other sectors, as well as economic activities of CON, TRA and OTH, should both decrease by 20%, which would be beneficial to the sustainability of the USWS.