Objective To evaluate the privilege of X-ray phase contrast imaging on the microstructure of mouse kidneys, and explore the imaging differences on kidney images obtained by DEI and in-line outline X-ray imaging (IOXI) with synchrotron radiation (SR) facility. Materials and Methods The SD mouse kidneys are taken as samples. DEI images were brought out at 4W1A beam line of BSRF and the in-line outline images were recorded at BL13W beam line of SSRF. Contrast of soft tissue and spatial resolution were selected mainly to evaluate the image quality. Results The kidney microstructures, which are usually hard to be visualized by conventional radiography, were recorded clearly with both of the imaging modalities. The kidney vessels of about 10 mu m in diameter were revealed, however more minute structures such as the renal glomeruli, were resolvable only in images taken with IOXI. Conclusion The phase contrast imaging has great potential to reveal the structures inside soft tissues which could achieve images of high quality for the tiny vessels without any administration of contrast media, and more microstructures of the mouse kidneys were demonstrated on IOXI. Due to the sample setup and fine images, the IOXI maybe well better manner in biological tissue imaging study.