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The signal-to-noise ratio (SNR) and spatial resolution are conflicting factors in conventional Brillouin optical time domain reflectometer (BOTDR) system. Golay complementary sequence with good autocorrelation properties, can be used as probe pulse, in order to achieve a higher SNR without compromising the spatial resolution of the system. This paper discusses the composition method of Golay complementary sequences, studies the principle applying Golay complementary sequences in BOTDR system. On this basis, a heterodyne detection BOTDR sensing system using Golay complementary sequences is designed and the system performances in time and frequency domain are simulated numerically. The results show that the method can improve the SNR of the system without degrading the spatial resolution.