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Three sweet potato varieties grew in natural high temperature (HT) and low temperature (LT) field soils. Their starch physicochemical properties were affected similarly by HT and LT soils. Compared with LT soil, HT soil induced the increases of granule size D[4,3] from 18.0–18.7 to 19.9–21.8 μm and amylopectin average branch-chain length from 21.9–23.1 to 24.1–24.7 DP. Starches from root tubers grown in HT and LT soils exhibited CA- and CC-type XRD pattern, respectively. Starches from root tubers grown in HT soil exhibited stronger lamellar peak intensities (366.8–432.0) and higher gelatinization peak temperature (72.0–76.8 °C) than those (176.2–260.5, 56.4–63.4 °C) in LT soil. Native starches from root tubers grown in LT soil were hydrolyzed more easily (hydrolysis rate coefficient 0.227–0.282 h−1) by amylase than those (0.120–0.163 h−1) in HT soil. The principal component analysis exhibited that starches from root tubers grown in HT and LT soils had significantly different physicochemical properties.