Heart sound segmentation is a key step before heart sound classification. It refers to the processing of the acquired heart sound signal that separates the cardiac cycle into systolic and diastolic, etc. To solve the accuracy limitation of heart sound segmentation without relying on electrocardiogram, an algorithm based on the duration hidden Markov model (DHMM) was proposed. Firstly, the heart sound samples were positionally labeled. Then autocorrelation estimation method was used to estimate cardiac cycle duration, and Gaussian mixture distribution was used to model the duration of sample-state. Next, the hidden Markov model (HMM) was optimized in the training set and the DHMM was established. Finally, the Viterbi algorithm was used to track back the state of heart sounds to obtain S1, systole, S2 and diastole. 500 heart sound samples were used to test the performance of our algorithm. The average evaluation accuracy score (F1) was 0.933, the average sensitivity was 0.930, and the average accuracy rate was 0.936. Compared with other algorithms, the performance of our algorithm was more superior. It is proved that the algorithm has high robustness and anti-noise performance, which might provide a novel method for the feature extraction and analysis of heart sound signals collected in clinical environments.