The partition function is a fundamental concept of equilibrium thermodynamics. It encodes the particle distribution at different energy levels within a thermal system. By modifying the partition function of a particle, the partition function of a protein conformational state has been obtained. According to the protein thermodynamic structure theory, a protein conformational state represents one thermal system within a protein. The partition function of it encodes the thermodynamic relation among the different conformational states of a protein. Many experimental observations and models in enzymology, biochemistry, and molecular biology have been summarized and reexamined by applying this concept. This paper discusses the following: (1) the partition function of a protein conformational state; (2) the conformation distribution between the two states; (3) the protein conformation distribution along the temperature gradient and the protein conformation stability curve; (4) the agonist efficiency and conformational distribution of a receptor along voltage; (5) the enzyme active conformation distribution along the temperature gradient; (6) the enzyme active conformation distribution with respect to protein flexibility; (7) a revision of the Arrhenius equation for enzymatic reactions; and (8) the biophysical nature of conformational equilibrium and deformation.