Scanning transmission X-ray microscopy (STXM) combined with an identical region in transmission electron microscopy (TEM) image has been used to detect the interior structure of individual thick multi-walled carbon nanotubes (MWCNTs). Two individual MWCNTs show similar morphology and diameters from the TEM images, while from the STXM spectra their interior structures have significantly different hollow parts. Moreover, the different hollow structures result in obviously different electronic structures which can be detected by X-ray absorption spectroscopy. Our results show an effective way to measure the inside hollow structure of thick MWCNTs.