As increasingly extensive applications of flexible manufacturing systems (FMSs) arise, their reliability allocation has been a research hot spot. But, since FMSs are always composed of transfer and buffer devices, production machines, and complex control systems, the large number of basic elements makes the number of variables and constraints of reliability-allocation optimization increase greatly, which leads to the difficulty and inefficiency of optimization. To solve the above problem, two dimension-reduction strategies are proposed for the FMS reliability optimization with low cost and a high level of reliability as the objectives, and they are the reliability-weight double-threshold qualification strategy (RWTS) and the bi-level optimization strategy (BLOS), respectively. Based on these two strategies, an overall reliability-allocation optimization model and a bi-level reliability-allocation optimization model are established based on the FMS reliability evaluation presented in our previous work, and their algorithms based on particle swarm optimization (PSO) are presented. In terms of their contributions, for the RWTS, thresholds of reliability and the weight index of each basic element are set to dynamically reduce the number of variables in each iteration of the optimization; for the BLOS, the overall reliability-allocation optimization problem for transitioning from the FMS to basic elements can be transformed into simpler allocation optimizations from the FMS to subsystems and from subsystems to basic elements, which have fewer variables, and this can largely improve the optimization convergence performance. Through applying this to a box-parts finishing FMS, compared with the traditional optimization method, the high efficiency and the good allocation effect of the optimization based on these two strategies for improving convergence speed are verified by the simulation results. The proposed method has great significance for FMS design due to its limited cost but high-reliability requirement.