Brillouin Optical Time Domain Reflectometry (BOTDR) has the ability to measure strain and temperature continuously in a fiber. It can be applied in the health structural monitoring for large-scale civil project such as bridges, dams and smart grid. Pulse coding/decoding technique can improve Signal to Noise Ratio (SNR) of BOTDR signal. However, at present, the data process of pulse coding/decoding technique generally relies on the software system. Such a system will be large in size and time consuming in the procedure of data transmission and processing. In this paper, we designed a dedicated hardware system with field programmable gate array (FPGA) using Simplex codes. We optimized the hardware structure and data processing algorithm to reduce the time cost. Experiments proved that this optimized design has the ability to obtain higher SNR of Brillouin backscattering signal than single pulse with less time consumption.