This paper presents a novel MEMS based DNA computer for solving SAT problems. No time-consuming sample preparation procedures and delicate sample applying equipment were required for the computing process. Moreover, experimental results show the bound DNA sequences can sustain the chemical solutions during computing processes such that the proposed method shall be useful in dealing with large scale problems. An algorithm based on a modified sticker model accompanied with a state-of-the-art MEMS-based microarray experiment is demonstrated to solve SAT problem which has long served as a benchmark in DNA computing. Unlike conventional DNA computing algorithms need an initial data pool to cover all correct and incorrect answers and further execute a series of separation procedures to destroy the unwanted ones, we built solutions in parts to satisfy one clause in one step, and eventually solve the entire Boolean formula through steps. Accordingly this algorithm greatly reduces the formation of unnecessary candidate solutions and shall be very practical as problem size grows. In this study, a novel MEMS-based technology including utilizing blank mask as the microarray substrate to prevent the self-fluorescent effect, a twin-mask back-side exposure process to improve the computing speed and a low-temperature backing process to prevent DNA damage during computing procedure. In addition, the minimal time requirement for DNA hybridization was also evaluated experimentally. The paper reports a novel computing method for solving SAT problem utilizing a state-of-art MEMS-based microarray. The advantage of this method is as the problem size scales up, it only needs to linearly increase the variety of sequences standing for variables and augment the array size. Therefore, while solving a complicated SAT problem, the numbers of DNA sample and the time for the computing process can be dramatically reduced with this approach.