Micro X-ray fluorescence (μXRF) imaging is powerful non-destructive technique for imaging distributions of nonradioactive elements within the body, including scanning X-ray fluorescence and X-ray fluorescence computed tomography. The spatial resolution is determined by the size of the X-ray focused beam spot. The μXRF instrumentation, which uses a simple pinhole aperture to restrict the incident beam size on the sample surface, has been established and opened to users at SSRF X-ray imaging beamline (BL13W). It has a typical spatial resolution ranging in diameter from 200 micrometers up toseveral millimeters. Ellipsoidal shaped single-bounce glass capillaries have been used as achromatic X-ray focusing optics for various applications at synchrotron beamlines, which can provide efficient and high demagnification focusing with large numerical apertures, large Working distance, the wide energy range of x-rays, small volume and so on. The support a wide range of applications, including Micro X-ray fluorescence, full-field transmission X-ray microscopy (TXM), etc. But the challenge is to make an accurate profile with small slope errors. In order to meet the requirements of users for μXRF imaging, the single bounce ellipsoidal glass mono-capillary was designed and fabricated and its performance was measured by an X-ray test. The focus spot and the gain of this mono-capillary were 14μm and 255 at 8 keV, respectively. The images of focal spot by detector showed that this fabricated mono-capillary had high quality and satisfied the requirement of the designed data for μXRF. The μXRF instrumentation has been established, based on ellipsoidal mono-capillary designed and fabricated by ourselves, andcarried out scanning X-ray fluorescence and X-ray fluorescence computed tomography experimental research at SSRF X-ray imaging beamline (BL13W). Firstly, the fluorescence spectrum of the trace elements copper, iron, calcium and zinc in the stroke rat brain by scanning X-ray fluorescence. Secondly, the Arsenic of standard solution and the rat brain were subjected to microX-ray fluorescence computed tomography. Two-dimensional slices of Arsenic element in solution and copper element in the rat brain by OSEM algorithm to reconstructed. This study demonstrates that the μXRF instrumentation is a powerful X-ray analytical microscope with the high resolution and high sensitivity μXRF capabilities available.