Abstract In this article, we investigate the hidden cross-correlation structures in Chinese stock markets and US stock markets by performing PCSE combined with PCA approach. It is suggested that PCSE can provide a more faithful and more interpretable description of the dynamic mechanism between time series than cross-correlation matrix. We show that this new technique can be adapted to observe stock markets especially during financial crisis. In order to identify and compare the interactions and structures of stock markets during financial crisis, as well as in normal periods, all the samples are divided into four sub-periods. The results imply that the cross-correlations between Chinese group are stronger than the US group in the most sub-periods. In particular, it is likely that the US stock markets are more integrated with each other during global financial crisis than during Asian financial crisis. However, our results illustrate that Chinese stock markets are not immune from the global financial crisis, although less integrated with other markets if they are compared with US stock markets.