This paper proposes a fully unsupervised methodology for the reliable extraction of latent variables representing the characteristics of lithium-ion batteries (LIBs) from electrochemical impedance spectroscopy (EIS) data using information maximizing generative adversarial networks. Meaningful representations can be obtained from EIS data even when measured with direct current and without relaxation, which are difficult to express when using circuit models. The extracted latent variables were investigated as capacity degradation progressed and were used to estimate the discharge capacity of the batteries by employing Gaussian process regression. The proposed method was validated under various conditions of EIS data during charging and discharging. The results indicate that the proposed model provides more robust capacity estimations than the direct capacity estimations obtained from EIS. We demonstrate that the latent variables extracted from the EIS data measured with direct current and without relaxation reliably represent the degradation characteristics of LIBs.