Highly crystalline, size-controlled Zn2SnO4 nanoparticles are synthesized by hydrothermal synthesis using two different mineralizers, viz., inorganic Na2CO3 and organic tert-butyl amine. The shape and surface properties of the two types of nanoparticles are totally different owing to the structure-directing abilities and the radicals in the mineralizers, even though both types of nanoparticles show a defect-free and highly crystalline structure. Na2CO3 induces faceted planar morphologies with negative surface charges, whereas tert-butyl amine induces roughly spherical shapes with positive surface charges; these changes have been analyzed by SEM, TEM, and zeta potential measurements. Electrochemical tests performed on these two types of nanoparticles indicate a capacity that gradually fades up to the 20th cycle due to the inevitable structural irreversibility. However, the specific discharge/charge capacities of both Zn2SnO4 anodes become almost constant after 20 cycles, and at 40th cycle, the specific discharge capacities of both nanoparticles are 521.4mAhg−1 for nanoparticles synthesized using tert-butyl amine and 448.0mAhg−1 for nanoparticles synthesized using Na2CO3 with Coulombic efficiencies higher than 96%. Such an excellent cycling stability and reversibility against lithium insertion/extraction can be attributed to the improved pulverization/agglomeration resistances of these materials, resulting from the surface residual charges, i.e., the repulsive forces between like-charged nanoparticles.