The complete synchronization of two chaotic systems and its secure communication have been considered based on DNA chemical reaction networks (DNA CRNs). There are concerns about the security of the single-level chaotic secure communication system. Thereby a multi-level secure communication scheme is put forward via DNA CRNs in this work. Firstly, a three-variable chaotic system that consists of catalysis, double, fasciation, and annihilation modules is constructed using DNA CRNs. Secondly, according to the stability principle of nonlinear systems, DNA CRNs are adopted to realize the coupling projection synchronization of three chaotic systems, and the synchronization results are discussed. Finally, sine and cosine signals are designed using DNA CRNs. These signals are added into three systems to realize multi-level encryption and decryption. Furthermore, the interference terms are taken into consideration to test the robustness of the system. The results show that the proposed scheme has high security, and can efficiently encrypt and decrypt biological signals through multi-level transmission in the presence of interference.