The amylose and amylopectin were separated by jackfruit seed starch (JFSS), and the same amylose (50%) was mixed with five different types of amylopectin to prepare JFSS (M1′, M5′, M6′, M11′, and BD′) with different degree of amylopectin polymerization. The effect of the degree of amylopectin polymerization on physicochemical properties of JFSS was investigated. M1′ had the lowest degree of amylopectin polymerization (189 506), while BD′ had the highest (431 481). As the degree of amylopectin polymerization increased, the syneresis, gelatinization enthalpy, peak viscosity, trough viscosity, breakdown, final viscosity, setback, relative crystallinity, and absorbance ratios of the five JFSS samples decreased from 72.87%, 16.59 J/g, 4 755 cP, 3 548 cP, 1 207 cP, 5 751 cP, 2 203 cP, 33.22%, and 1.56 (M1′) to 66.79%, 11.04 J/g, 2 717 cP, 1 971 cP, 746 cP, 3 158 cP, 1 187 cP, 27.94%, and 1.45 (BD′), respectively. However, the transition temperatures and pasting temperature increased from 48.19, 60.39, 75.32 ℃and 77.55 ℃(M1′) to 52.39, 64.54, 78.47, and 81.60 ℃ (BD′), respectively. The results of the freeze-thaw stability, thermal properties, crystalline structure, and short-range molecular order indicated that the degree of amylopectin polymerization is an important structural factor that can affect thephysicochemical properties of starch.