Empty elements (EEs) play a critical role in Chinese syntactic, semantic and discourse analysis. Previous studies employ a language-independent sentence-level approach to EE recovery, by casting it as a linear tagging or structured parsing problem. In comparison, this paper proposes a clause-level hybrid approach to address specific problems in Chinese EE recovery, which recovers EEs in Chinese language from the clause perspective and integrates the advantages of both linear tagging and structured parsing. In particular, a comma disambiguation method is employed to improve syntactic parsing and help determine clauses in Chinese. In this way, the noise introduced by sentence-level syntactic parsing and multiple EEs in the same position of a linear sentence can be well addressed. Evaluation on Chinese Treebank 6.0 shows the significant performance improvement of our clause-level hybrid approach over the state-of-the-art sentence-level baselines, and its great impact on a state-of-the-art Chinese syntactic parser.