This paper investigates the experimental and numerical analysis of the macroscopic and microscopic spray characteristics of biodiesel, dimethyl ether (DME), and biodiesel -ethanol blended fuels in the common-rail injection system. For the experimental study of the macroscopic spray characteristics, spray developing process and spray tip penetration of the test fuels were visualized using a laser sheet method. In order to analyze the atomization characteristics of the three kinds of fuels, the microscopic characteristics such as the Sauter mean diameter (SMD) at the measuring point in the spray, frequency distribution of the number of droplets according to droplet size, and the relation of droplet diameter and Weber number were compared with numerical results obtained by the calculation. Based on the results of the investigation, the experimental results for the atomization characteristics of different fuels show a good agreement with the predicted results. In this work, the effects of different alternative fuels such as biodiesel, dimethyl ether, and biodiesel -ethanol blended fuel on the spray atomization characteristics were simulated by the KIVA code and the calculated results using the hybrid model combined with the primary and secondary breakup were compared and analyzed with the experimental results in terms of the shape of spray, spray evolution processes, and SMD distribution.