In the financial transaction system centering on blockchain technology, institutions at different levels have different powers and roles, so that they have dissimilar private contents to protect. Taking supply chain financing as an example, a multi-level blockchain system is proposed in this paper. The main steps of building the system are as follows: Firstly, commercial banks and regulatory authorities cooperatively establish a risk control model by Federal Learning. Secondly, the private transaction information will be preserved by zero-knowledge proofs for downstream suppliers. Finally, an architecture of multi-level blockchain is designed to supervise the financial trading for guaranteeing credibility. The experimental results show that the system is more beneficial to privacy protection. By incorporating Federal Learning, it can provide stronger security and more reliable risk control. Further, that can also improve the efficiency and performance of the financial transaction system.