To protect data privacy in blockchain cross-chain transactions, this study proposes a privacy protection scheme based on homomorphic encryption. The scheme improves the homomorphic encryption algorithm to support floating-point operations while retaining the additive homomorphic property of the original algorithm, and it supports any number of addition operations to realize the privacy protection of cross-chain transaction amounts. To prevent security threats to transactions posed by mismanagement or loss of the private key with homomorphic encryption, a private key sharing mechanism based on Shamir’s secret sharing algorithm is introduced into the scheme. This mechanism prevents untrustworthy nodes from sending malicious values to recover the private key by adding ECDSA digital signatures to verify the private key share. It also considers the dynamic update of the private key share after a node drops or leaves to prevent node collusion. Security analysis and experimental verification show that the proposed scheme can effectively protect privacy in cross-chain transactions.