Biomolecular-carbon nanotube (CNT) complexes are of great importance in biological and biomedical devices, and recently spontaneous encapsulation of biomolecules into CNTs has attracted great interest. In this work, we explored the diameter selectivity of the protein encapsulation in CNTs via molecular dynamics simulations, and the free energy changes of the systems were calculated for mechanism exploration. It is proved that there is an optimal tube size which provides the most effective encapsulation for a given protein molecule, and the encapsulations in the overlarge and overcrowded tubes are hindered by different factors based on the analysis of system energy contribution. In addition, the significance of the solvents for the system is also of concern.