The structural synthesis of planetary gear trains (PGTs) lays an important foundation for creating new mechanisms of transmission systems. Most existing studies focused on the synthesis of single degree-of-freedom (DOF) PGTs, while the synthesis of multi-DOF PGTs is very limited. This paper presents a matrix-based method for the automatic synthesis of non-fractionated PGTs with both single and multiple DOFs. First, the concept of a modified dual graph is proposed, based on which a new and simple method is presented to efficiently detect fractionated graphs. Then, the concepts of vertex adjacency index and moment matrix are defined, and a reliable algorithm is proposed to detect isomorphic graphs. Finally, a matrix-based method for the automatic synthesis of non-fractionated PGTs is presented, and the complete databases of non-fractionated PGTs with 3–9 links and 1–3 DOFs are generated for the first time. The creative design of mechanisms of 6-speed automatic transmission (AT) is taken for instance to illustrate how to design new transmission systems based on our databases.