The conformational transition of cyclohexylene ring has been recognized as the secondary transition of polyesters containing this aliphatic ring structure. Previously, the stereochemistry, i.e., trans/cis ratio, has been identified as an important factor that has a significant impact on the conformational transition of the cyclohexylene ring. In this paper, we have proposed and proved the side chain effect as another important factor that plays the same role as the stereochemistry, due to the fact that the conformational transition of the ring is usually associated with the coupled motion of it with neighboring unit. Our strategy is to design and synthesize a series of polyesters with 1,4-cyclohexanedicarboxylic acid and diols with different side chains. Polyester without any side chain has the lowest secondary relaxation temperature (T (beta) ). Incorporation of asymmetric short side chain will result in increased T (beta) , since it will reduce the coupled motion of the neighboring unit with the cyclohexylene ring during the conformational transition process, and thus reduces the flexibility of the chain and increases steric hindrance. However, further incorporation of long side chain will result in decreased T (beta) because of the plasticization effect. Moreover, we also found that polyesters with low T (beta) tend to have not only better impact strength, but also good ductility and elasticity. Our study enables people to take advantage of the cyclohexylene ring structure for the design and synthesis of thermoplastic and elastomer with better performance.