In this article, the multi-wavelength traveling wave model with rate equations are utilized to simulate the ASE spectrum in ytterbium-doped gain media. By solving the rate equations in time domain and in 0.9-1.1 µm region, the model shows how the fiber length and amplifier configuration can affect amplifier operation and change the peak gain or bandwidth. The effect of various parameters including ratio of core area over inner cladding area, doping profile, pump wavelength and pumping scheme on the ASE spectrum are investigated. For a given pump power, wavelength, core over cladding area ratio and fiber concentration, by increasing the YDF length from 10 to 400 cm, the dominant peak in ASE spectrum, shifts from 1055.42 to 1074 nm. Meanwhile the FWHM of the observed spectra decreases from 48 nm to 33 nm. For a given fiber length and by a sufficient increase of the pumping wavelength, we can further decrease the ASE (fluorescence) bandwidth by about 15 nm. These new results are consistent with those obtained from our experiments. In conclusion, by adjusting the fiber length, the pumping scheme and the wavelength, one can either form a nearly broad, symmetric and smooth or a narrow high gain spectrum.