When several traditional flow-shop lines operate in parallel, the operation mode with no communication between production lines will no longer be the optimal production paradigm. This paper describes matrix manufacturing systems (MMS) in a general manner from the perspective of related works, comparing different manufacturing organizational forms and their characteristics. Subsequently, MMS are extracted during the parallel production of multiple surface mount technology (SMT) lines. An overall equipment effectiveness (OEE) online calculation model and a collaborative optimization method are proposed based on the OEE of the MMS. The innovative idea of this study is to divide existing multiple parallel SMT lines into MMS. The efficiency of each matrix unit (MU) was calculated, and a collaborative optimization method was proposed based on an indicator (OEE). In this paper, an example of eight SMT lines is presented. The partitioning of MUs, OEE calculation of each MU, and the low OEE unit collaborative optimization method are described in detail. Through a case study, the architecture of the collaborative optimization model for the MMS was constructed and discussed. Finally, the improvement in the OEE proved the effectiveness and usability of the proposed architecture.