Objective To study the collapse of biomolecules, focusing on the effect of the composition of chain, temperature and stiffness on the chains self-assembly. Method A coarse grained molecular dynamics method is adopted to simulate the collapse of the biomolecules with two kinds of sequence composition. Results We find that the inhomogeneity can induce network-like microstructures in the equilibrium structure of chain. And the stiffness of chain determines the global structure of chains. When the chain is soft, both homogeneous and inhomogeneous chains collapse to globular structure; however, when the chain is stiff, the chains evolve to rod-like or toroidal structure. We also find that the inhomogeneous chain is more sensitive to temperature change in comparison with the homogeneous chain. Conclusions This study will help understand the mechanisms of self-assembly and relationship between function and structure of biomolecules.