The amount of outsourced data grows rapidly. In recent years, cloud service providers integrate data deduplication systems with convergent encryption (CE) methods, in which a file encryption key is determined by its own content instead of the secret of a specific user, to save the storage cost and ensure the security of outsourced data. However, present secure deduplication systems failed to deal with data modifications efficiently. We observe that when a client makes small changes on an existing file, the current chunking algorithms cannot effectively detect the similarities and always create chunks with largely overlapped contents. It reduces data deduplication ratios and results in unnecessary overhead. In this paper, we propose Sed-Dedup, an efficient secure delta encoding deduplication system to address this problem. In Sed-Dedup, we introduce a novel delta encoding approach to store modified contents in delta files and leave the original files intact. Two schemes with different encoding policies are designed. Both of them can solve the issue and improve the secure deduplication performance. To evaluate the performance, we implement a prototype and conduct extensive experiments based on synthetic and real-world datasets. Our experimental results show that Sed-Dedup is superior to the state-of-the-art secure deduplication systems.