This study aimed to assess the phenotypic and histological characteristics of leaves, stems, and roots of sweet potato (‘Hopungmi’ and ‘Sodammi’, Korean cultivars) under the low-temperature conditions induced by early transplanting. In leaves, early transplanting (ETP) led to reductions in vascular bundle width (from −22.6% to −53.7%), xylem diameter (from −51.6% to −52.6%), palisade parenchyma thickness (from −31.3% to −31.5%), and the palisade parenchyma thickness-to-leaf thickness ratio (from −31.2% to −32.1%), while the total leaf thickness remained unchanged. Principal component 1 (PC1: 69.7%) was positively correlated with vascular characteristics and palisade parenchyma thickness, reflecting enhanced development under optimal transplanting (OTP) and greater photosynthetic capacity. These findings indicate that low temperatures hinder palisade parenchyma development. In stems, ETP reduced stem radius (from −20.3% to −42.1%) and the pith-to-stem radius ratio (from −21.0% to −25.3%) but increased the xylem-to-stem radius ratio (from +45.8% to +47.1%) and the collenchyma-to-stem radius ratio (from +61.5% to +84.7%). PC1 (45.7%) showed positive correlations with xylem and collenchyma ratios and negative correlations with stem radius and pith ratio, suggesting that these anatomical adjustments helped maintain stem rigidity under stress. In roots, ETP significantly reduced root radius (from −78.0% to −94.5%), vascular radius (from −83.9% to −96.9%), cortex thickness (from −68.9% to −80.7%), and the vascular-to-root radius ratio (from −28.6% to −44.7%), while increasing the cortex-to-root radius ratio (from +53.0% to +248.0%). PC1 (93.8%) was positively associated with vascular characteristics and cortex thickness and negatively associated with the cortex-to-root radius ratio. Overall, the low temperatures resulting from early transplanting altered the anatomical structures of leaves, stems, and roots, indicating suboptimal conditions for storage root development. In particular, the vascular bundle radius of sweet potato roots was identified as a crucial indicator for evaluating storage root development, which can be utilized in future breeding strategies.