In a hydrothermal and solvothermal system at 120 °C, cylinder-like and rod-like nanostructures of hydrate copper oxalate (CuC2O4·xH2O) can be thoroughly synthesized in the absence of any shape-controlling additives, respectively. The self-assembly of primary nanocrystals has been investigated considering the polarity of reaction medium, and in the chemical formula of CuC2O4·xH2O the average x value of crystal water is estimated to discuss the superior lithium storage capability of hydrate products. The results show that cylinder-like aggregate of CuC2O4·xH2O (x ∼ 0.14) possesses an initial discharge capacity of 920.3 mAh g−1 with a residual capacity of 970.0 mAh g−1 at 200 mA g−1 over 100 discharge–charge cycles, while rod-like aggregate with a x value of ∼0.53 per chemical formula exhibits a higher initial capacity of 1211.3 mAh g−1 and a lower retention of 849.3 mAh g−1 under the same conditions. Furthermore, time-dependent measurements present a novel crystal-to-amorphous transformation of active substances, suggesting a positive effect of unavoidable crystal water on the superior lithium storage capability of nanostructured CuC2O4·xH2O.