The rapid growth of cloud computing has intensified the need for secure data outsourcing solutions. Fully homomorphic encryption (FHE) offers a promising approach by enabling computations on encrypted data without exposing the plaintext. This paper advances the synthesis of homomorphic Boolean circuits, a pivotal component in FHE, by addressing two major limitations of existing methods: (1) effectively exploiting large-fan-in logic gates to achieve more compact circuit designs, and (2) leveraging the multi-value functional bootstrapping technique to further reduce computational overhead in evaluating Boolean functions. The proposed homomorphic circuit synthesis flow effectively and efficiently improves homomorphic evaluation efficiency. Experimental results show that, compared to the state-of-the-art, our flow achieves 1.36× faster synthesis time and reduces execution cost by an average of 29.94%, with a maximum reduction of 76.02%.