Cell staining is a typical procedure for assessing the distribution and density of intracellular components. In this work, a label-free alternative is developed and verified using impedance cytometry to characterize the loss of intracellular components in Euglena gracilis (E. gracilis) cells. By inhibiting chloroplast synthesis, the number of chloroplasts in single cells are reduced gradually, as is the density of intracellular components. As a result, low-frequency impedance signals (0.5 MHz) are shown to assess the cell morphology. With increasing voltage frequency (i.e., > 1 MHz), the resistance of the cell membrane lowers, and the cell membrane eventually becomes transparent to impedance detection. The magnitude and morphology of impedance signals (6 MHz) get the dependance on the density and distribution of intracellular components, respectively. Additionally, impedance-based cell phenotyping reveals that the shrinking of intracellular components and cell volume can cause two distinct declines in the high-and low-frequency electrical diameter of single cells, respectively. This conclusion is confirmed by simulation results and the time course of the changes in electrical diameters and electrical opacity. To sum up, our findings indicate that impedance cytometry and our analysis method can be further refined to serve as a powerful and non-invasive tool for assessing intracellular components at the single cell level.