Manufacturing product and providing service in a quick and economic way is the common goal of enterprises under the impact of globalization automation. In the methods of lowering cost and increasing productivity, facilities layout is of the most important. How to arrange, distribute and integrate the facilities of an enterprise in order to maximize the performance is particularly important. It is costly and time consuming to rearrange facilities layout after mass production, and largely impact the operation of enterprise negatively. Thus, this study applying Hilbert space filling layout method to reach better space utilization by considering department placement direction, geometry, size, and the order of placement. The proposed model also contemplate material flow factor cost (MFFC), shape ratio factor (SRF), area utilization factor of overall layout, and even the quantified adjacency of departments to derive minimal total layout cost by genetic algorithm. By introduce the model to a real case, we find it suitable for the complex and tedious production and material flow, especially in the small and medium enterprises.