Considering the scarcity of research on 3D medical image encryption, this paper proposes a novel 3D medical image encryption scheme based on biometric key and cubic S-box. To enhance the data security, biometric keys are utilized to overcome the limitations of traditional methods where secret keys with no practical meaning, fixed length, and finite key space, while cubic S-box is constructed to increase the nonlinearity of image cryptosystem. The proposed cryptosystem mainly consists of four phases: pseudo-random sequence generation, confusion, substitution, and diffusion. Firstly, the stepwise iterative algorithm based on coupled chaotic systems is utilized for generating pseudo-random sequences for confusion and diffusion. Secondly, the confusion algorithm based on multiple sorting can scramble pixel positions in 3D images. Thirdly, guided by the designed cubic S-box, pixel substitution is executed sequentially. Lastly, the diffusion algorithm based on ECA and finite field multiplication is capable of increasing the plaintext sensitivity of cryptosystem by concealing the statistical characteristics of plaintext. Simulation experiments performed on multiple 3D medical images demonstrate that the proposed encryption scheme exhibits favorable statistical performance, sufficiently large key space, strong system sensitivity and robustness, and can resist various typical cryptographic attacks.