To analyze the structure complexity of chaotic sequence,structure complexity of three kinds of different chaotic sequences is investigated based on Spectral Entropy and Wavelet Entropy algorithm.The complexity of several typical discrete chaotic systems is calculated respectively,including Logistic map,Henon map and TD-ERCS system.Using sliding window method,complexity stability of chaotic systems along the time evolution is analyzed.The results show that:1) Both of the two algorithms are effective for measuring structure complexity of chaotic sequences.2) The complexity of TD-ERCS chaotic sequence is nearly equal to that of Logistic map,and it has good stability for parameter m.3) The bigger the complexity of a system is,the better the time stability is.It provides an experimental basis for the application of chaotic sequences in the field of information security.