Collaborative perception has been proven to improve individual perception in autonomous driving through multi-agent interaction. Nevertheless, most methods often assume identical encoders for all agents, which does not hold true when these models are deployed in real-world applications. To realize collaborative perception in actual heterogeneous scenarios, existing methods usually align neighbor features to those of the ego vehicle, which is vulnerable to noise from domain gaps and thus fails to address feature discrepancies effectively. Moreover, they adopt transformer-based modules for domain adaptation, which causes the model inference inefficiency on mobile devices. To tackle these issues, we propose CoDS, a Collaborative perception method that leverages Domain Separation to address feature discrepancies in heterogeneous scenarios. The CoDS employs two feature alignment modules, i.e., Lightweight Spatial-Channel Resizer (LSCR) and Distribution Alignment via Domain Separation (DADS). Besides, it utilizes the Domain Alignment Mutual Information (DAMI) loss to ensure effective feature alignment. Specifically, the LSCR aligns the neighbor feature across spatial and channel dimensions using a lightweight convolutional layer. Subsequently, the DADS mitigates feature distribution discrepancy with encoder-specific and encoder-agnostic domain separation modules. The former removes domain-dependent information and the latter captures task-related information. During training, the DAMI loss maximizes the mutual information between aligned heterogeneous features to enhance the domain separation process. The CoDS employs a fully convolutional architecture, which ensures high inference efficiency. Extensive experiments demonstrate that the CoDS effectively mitigates feature discrepancies in heterogeneous scenarios and achieves a trade-off between detection accuracy and inference efficiency.