Zero-shot voice conversion (VC) aims to transform the timbre of a source speaker into any previously unseen target speaker, while preserving the original linguistic content. Despite notable progress, attaining a degree of speaker similarity and naturalness on par with ground truth recordings continues to pose great challenge. In this paper, we propose CTEFM-VC, a zero-shot VC framework that leverages Content-aware Timbre Ensemble modeling and Flow Matching. Specifically, CTEFM-VC disentangles utterances into linguistic content and timbre representations, subsequently utilizing a conditional flow matching model and a vocoder to reconstruct the mel-spectrogram and waveform. To enhance its timbre modeling capability and the naturalness of generated speech, we propose a context-aware timbre ensemble modeling approach that adaptively integrates diverse speaker verification embeddings and enables the joint utilization of linguistic and timbre features through a cross-attention module. Experiments show that our CTEFM-VC system surpasses state-of-the-art VC methods in both speaker similarity and naturalness by at least 18.5% and 7.0%.