Poly(cyclohexane dimethylene-co-2,2,4,4-tetramethyl cyclobutylene terephthalate) (PCcBT) is a highly transparent, safe, and heat-resistant copolyester and has been commercialized to replace bisphenol A polycarbonate in many kinds of applications. However, there are still some shortcomings in its synthesis and processing such as 2,2,4,4-tetramethyl-1,3-cyclobutanediol (CBDO) sublimation, composition deviation, and relatively poor thermal stability. In this study, 2-methyl-1,3-propanediol (MPO) or 3-methyl-1,5-pentanediol (Pe′DO) were used as diol comonomers instead of cyclohexane dimethanol to synthesize poly(3-methyl-1,5-pentylene-co-2,2,4,4-tetramethyl cyclobutylene terephthalate) and poly(2-methyl-1,3-propylene-co-2,2,4,4-tetramethyl cyclobutylene terephthalate) (PMcBT) copolyesters. The effects of comonomers on solubility and sublimation of CBDO and the robustness of polymerization as well as thermal stability during polymerization and processing were examined with emphasis. The presence of Pe′DO and MPO facilitated CBDO dissolution and avoided CBDO sublimation and pipeline blocking, possibly due to a stronger intermolecular interaction between CBDO and Pe′DO or MPO. The deviations of composition and cistrans ratio between the CBDO monomer and the copolymers were also reduced. The presence of a Pe′T or MT repeat unit endowed the copolymers with improved thermal stability, resulting in much less undesired melt foaming and volume expansion during melt polycondensation and processing. These copolymers are colorless, highly transparent, and heat-resistant materials with Tg up to 145 °C. Among them, PMcBT exhibits the best overall performance, displaying more balanced mechanical properties and better optical properties over commercialized PCcBT.