In order to reduce the relatively high probability of missed and false detection in traditional hard threshold setting algorithm, improve the anti-interference performance of Transform Domain Communication System (TDCS), an adaptive N-sigma amplitude spectrum shaping algorithm was proposed. The amplitude information of environment power spectrum was got according to spectrum sensing, the mean and standard deviation of the environment power spectrum were calculated. According to the correlation theory of normal distribution, the threshold was adaptively set. Therefore, when the electromagnetic environment changed, the mean and standard deviation would be readjusted and the threshold would be updated. The simulation results show that, compared to the traditional hard threshold setting algorithm, the threshold setting of the adaptive N-sigma amplitude spectrum shaping algorithm is more flexible and accurate, which can reduce the missed detection probability and false detection probability of interference and improve the overall anti-interference performance of the system.