Synchrotron-based soft X-ray tomography (SXT), providing three-dimensional morphology and quantitative distribution of linear absorption coefficient (LAC) of the imaged objects, is widely used in many fields to obtain ultra-structure images, especially in cellular imaging. Off-line fluorescence microscopies (FMs) are combined to identify the type of organelles and status of cells. However, deformation and displacement usually occur during the transfer and loading process, which decreases the precision of two-modal images’ registration. In this paper, we report on an on-line FM, at the SXT station (BL07W) of the National Synchrotron Radiation Laboratory (NSRL), which avoids deformation and displacement. Therefore, researchers can easily find the sample and take the useful data without tedious post-processing. Combining SXT with on-line FM, we achieved the identification and high-resolution imaging of an apoptotic cell. The experiments revealed that the LAC of the nucleus of the apoptotic cell was larger than that of a normal cell, which could be explained by nucleus pyknosis of the apoptotic cell.