Video Question Answering (VideoQA) is challenging as it requires capturing accurate correlations between modalities from redundant information. Recent methods focus on the explicit challenges of the task, e.g. multimodal feature extraction, video-text alignment and fusion. Their frameworks reason the answer relying on statistical evidence causes, which ignores potential bias in the multimodal data. In our work, we investigate relational structure from a causal representation perspective on multimodal data and propose a novel inference framework. For visual data, question-irrelevant objects may establish simple matching associations with the answer. For textual data, the model prefers the local phrase semantics which may deviate from the global semantics in long sentences. Therefore, to enhance the generalization of the model, we discover the real association by explicitly capturing visual features that are causally related to the question semantics and weakening the impact of local language semantics on question answering. The experimental results on two large causal VideoQA datasets verify that our proposed framework 1) improves the accuracy of the existing VideoQA backbone, 2) demonstrates robustness on complex scenes and questions.