With outstanding capability to express uncertain information, complex evidence theory can be widely applied in a multiplicity of fields of representation and fusion of information. However, in complex evidence theory, conflict measurement is still an open issue. To address this problem, we propose a new complex belief χ² divergence measure (CBχ²), which has the ability to measure the discrepancy between the complex basic belief assignments (CBBAs). In addition, the proposed CBχ² divergence measure satisfies the properties of nonnegativity, nondegeneracy and symmetry. Particularly, when the CBBA degenerates to classical basic belief assignments (BBA), the proposed divergence can also measure the conflict well. On this basis, a novel BEoCBχ²D is proposed to measure the complexity of cardiac interbeat interval time series in biological system. An application in cardiac interbeat interval time series analysis demonstrates that BEoCBχ²D has better accuracy.