Causal structure learning can reveal the causal mechanism behind natural systems. It is well studied that the multiple domain data consisting of observational and interventional samples benefit causal identifiability. However, for non-stationary time series data, domain indexes are often unavailable, making it difficult to distinguish observational samples from interventional samples. To address these issues, we propose a novel Latent Intervened Non-stationary learning (LIN) method to make the domain indexes recovery process and the causal structure learning process mutually promote each other. We characterize and justify a possible faithfulness condition to guarantee the identifiability of the proposed LIN method. Extensive experiments on both synthetic and real-world datasets demonstrate that our method outperforms the baselines on causal structure learning for latent intervened non-stationary data.