The time-triggered communication paradigm is a cost-efficient way to meet the real-time requirements of cyber-physical systems. It is a non-deterministic polynomial NP-complete problem for multi-hop networks and non-strictly periodic traffic. A two-level scheduling approach is proposed to simplify the complexity during optimization. In the first level, a fuzzy-controlled quantum-behaved particle swarm optimization (FQPSO) algorithm is proposed to optimize the scheduling performance by assigning time-triggered frame instances to the basic periods of each link. In order to prevent population from high aggregation, a random mutation mechanism is used to disturb particles at the aggregation point and enhance the diversity at later stages. Fuzzy logic is introduced and well designed to realize a dynamic adaptive adjustment of the contraction–expansion coefficient and mutation rate in FQPSO. In the second level, we use an improved Satisfiability Modulo Theories (SMT) scheduling algorithm to solve the collision-free and temporal constraints. A schedulability ranking method is proposed to accelerate the computation of the SMT-based incremental scheduler. Our approach can co-optimize the jitter and load balance of communication for an off-line schedule. The experiments show that the proposed approach can improve the performance of the scheduling table, reduce the optimization time, and reserve space for incremental messages.