Super-Kamiokande is a large water Cherenkov detector located approximately 1,000 m underground in Kamioka, Japan. The detector is a cylindrical tank 39.3 m in diameter and 41.4 m high, filled with about 50 kton of gadolinium loaded water. We measured $^9$Li isotopic nuclei produced by muon spallation using the data taken from 2020 to 2022 by the Super-Kamiokande detector with 0.011% gadolinium concentration in water. Cosmic-ray muons that penetrate the detector form hadron showers in water and secondary hadrons produce unstable radioisotopes through the spallation. Among those spallation products, $^9$Li is a long-lived radioactive isotope with a lifetime of about 0.26 seconds. It emits an electron and a neutron at a branching ratio of 50.8%, which is difficult to distinguish from the inverse beta decay caused by electron antineutrinos. Therefore, $^9$Li is one of the main background sources in the observation of diffuse supernova neutrino background. In this study, the energy spectrum of the electrons was measured with a threshold at 4.5 MeV which is lowered from the previous result with pure water. We will report the analysis method and results.