As a novel partial substitution and surface modification process, we focused on a step-by-step (double-step) supersonic-wave treatment in a Zn-containing aqueous solution without any heat-treatments, and performed the treatment on LiMn2O4 powder. From XRD measurements, it was demonstrated that the lattice constant of LiMn2O4 decreased slightly by the treatments, indicating a partial substitution of Zn for Mn. It was also suggested by SEM–EDX and XPS that Zn was well dispersed in/on the samples and their surfaces were modified by Zn compounds. Such a partial substitution and surface modification was supported by crystal structure analysis based on the Rietveld method using neutron diffraction. Cycle performance of LiMn2O4 was significantly improved by the step-by-step supersonic-wave treatments. In the processes, it was especially effective for the improvement to apply lower and higher frequencies at the first and second steps, respectively, keeping the power higher. The cathode property improvement was considered due to the partial substitution and the surface coating caused by the step-by-step supersonic-wave treatments. From the investigation on the cathodes and electrolytes after the cycle tests, it was suggested that the crystal structure of LiMn2O4 was stabilized by the treatments.