This paper focuses on the production scheduling in MEMS manufacturing. The whole MEMS production process can be broken into 3 sub-processes, i.e., the front-end process, the wafer cap process and the back-end process. Every wafer processed by the front end process needs to be bonded with a wafer cap that are manufactured by the wafer cap process, and then it will be sent to the back-end process. Therefore how to synchronize the release of wafers into the front end as well as the wafer cap process becomes an important topic. An ineffective coordination will create larger WHIP and longer cycle time. In this paper, four different synchronization rules are developed and they are evaluated together with seven dispatching rules. The performance measures considered are cycle time, throughput rate and WHIP. A visual interactive simulation model is constructed to imitate the production line. The simulation results indicate that the synchronization rules have more significant impact than the dispatching rules on the performance of MEMS manufacturing.