The crystal structure analysis of a cycloaliphatic polyester, poly(butylene-trans-1,4-cyclohexane dicarboxylate) (PBCE), is performed by X-ray fiber diffraction. Depending on the cooling condition, two crystal forms are identified (α and β). The α form is obtained by slow cooling from the melt, while the β form is generated during fast cooling. The α form has a triclinic unit cell with a P1̅ space group, with parameters of a = 5.46 Å, b = 6.89 Å, c = 13.51 Å, α = 138.37°, β = 109.42°, and γ = 63.30°. One PBCE chain is located in the unit cell with the chair conformation aliphatic rings and all-trans-conformation methylene segmental parts. The structural transition and polymorphic transition during the heating and stretching process of PBCE are investigated by in-situ X-ray scattering. During heating, both the α and β forms show significant lattice distortion and eventually transform directly into the isotropic melt state. The volumetric thermal expansion coefficient of the PBCE α form was twice that of its unsaturated analogue, poly(butylene terephthalate). On the other hand, the irreversible β−α transition occurs during stretching, indicating that the β form is a metastable phase.