It is important to control the femtosecond laser filamentation and the supercontinuum (SC) for their potential applications. The use of axicon is beneficial to the filamentation elongation and SC enhancement, because the axicon can convert the incident laser into a Bessel beam and forms a unique longer depth of focus region. On the other hand, the flattened laser beam which has a uniform distribution of the beam intensity, can propagate in condense media with a higher incident energy than that of Gaussian laser beam. It has unique advantages in forming a SC with high energy and high conversion efficiency. In this paper, we combine the use of axicon and the flattened laser beam to form filament and SC in fused silica. First, we study the filamentation generated by the Gaussian beam and the flattened beam, respectively, with the same incident pulse energy (672 μJ). The results show that the flattened beam can generate filament with relative uniform intensity distribution in the focal depth of the axicon and the intensity is relatively smaller than that of the Gaussian beam. It suggests that the flattened laser beam can propagate in fused silica with a higher energy than Gaussian beam. Second, we study the filamentation of the flattened beam of 1.319 mJ. In this case, the filament intensity is close to that of the Gaussian beam with 672 μJ. Moreover, the filamentation of the flattened beam with 1.319 mJ is longer and the intensity distribution is more uniform than that of the Gaussian beam with 672 μJ. Therefore, a flattened laser beam can generate the SC with a higher energy than that of the Gaussian beam in fused silica. The comparison of the spectra shows that the relative spectral intensity of flattened beam with 1.319 mJ in the range of 550–700 nm is much higher than that of the Gaussian beam with 672 μJ. The conversion efficiency of the Gaussian beam and the flattened beam is 32.58% and 39.59%, respectively. It can be seen that the flattened laser beam has advantages not only in generating long and uniform filament, but also in generating the intense SC. This approach is helpful to many applications, such as white light LIDAR and micro-nano processing.