Storage of potato tubers is an essential stage of the supply chain, from farm to consumer, to efficiently match supply and demand. However, the quality and yield of potatoes are influenced by physiological changes during storage. This study tested the physiological and biochemical indices in three potato varieties (YunSu 108, YunSu 304 and YunSu 306) during their dormancy periods. Three potato varieties with different dormancy periods were used to follow changes in starch, protein and several enzymes during storage. The starch and sugar content of the long-dormant variety (YunSu 108, LDV) were stable, whereas those of the short-dormant variety (YunSu 306, SDV) were variable. Starch synthase activity in the three varieties was initially high, then decreased; the starch content of LDV was relatively stable, that of the medium-dormant variety (YunSu 304, MDV) increased with storage time and peaked at sprouting, and that of SDV was low but variable. The sucrose synthase activity of LDV was significantly higher (p < 0.05) than MDV and SDV in the middle storage period. Two spikes were observed in the invertase activity of SDV, whereas those of MDV and LDV were stable. The reducing sugar content of LDV increased significantly before sprouting, that of MDV slowly decreased and that of SDV dropped sharply. During the whole storage period, pectinase activity in LDV did not change significantly, whereas pectinase in MDV and SDV decreased. The cellulase and protein contents initially increased and then decreased in LDV, and steadily decreased in MDV and SDV. The metabolic indices related to starch and sugar in the LDV were relatively stable during storage, whereas those of the SDV varied greatly. SDV showed increased sucrose, reducing sugars and cellulose; LDV PCA plots clustered in the positive quadrant of PC1 and the negative quadrant of PC2, with increased protein, sucrose synthase and starch; MDV had increased soluble starch synthase.