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A fundamental challenge of recommendation systems (RS) is understanding the causal dynamics underlying users' decision making. Most existing literature addresses this problem by using causal structures inferred from domain knowledge. However, there are numerous phenomenons where domain knowledge is insufficient, and the causal mechanisms must be learnt from the feedback data. Discovering the causal mechanism from RS feedback data is both novel and challenging, since RS itself is a source of intervention that can influence both the users' exposure and their willingness to interact. Also for this reason, most existing solutions become inappropriate since they require data collected free from any RS. In this paper, we first formulate the underlying causal mechanism as a causal structural model and describe a general causal structure learning framework grounded in the real-world working mechanism of RS. The essence of our approach is to acknowledge the unknown nature of RS intervention. We then derive the learning objective from our framework and propose an augmented Lagrangian solver for efficient optimization. We conduct both simulation and real-world experiments to demonstrate how our approach compares favorably to existing solutions, together with the empirical analysis from sensitivity and ablation studies.