Accurate estimation of time-varying treatment effects is crucial for optimizing interventions in personalized medicine. However, observational data often contains complex confounding bias and temporal complexities, making counterfactual estimation challenging. We propose Counterfactual Estimation via Temporal-Aware Intervention Networks (TAIN), a novel model that introduces an Intervention-aware Functional Convolution kernel to emphasize the role of treatments and capture complex temporal treatment interactions. TAIN addresses confounding bias from a domain generalization perspective, approximating the unknown target domain using adversarial examples and incorporating Sharpness-Aware Minimization to derive a generalization bound. This approach is more suitable for longitudinal settings compared to existing methods inspired by domain adaptation techniques due to inherent differences between static and longitudinal contexts. Experiments on simulated datasets demonstrate TAIN's superior performance compared to state-of-the-art models for counterfactual estimation over time.