A model was established to analyze the side bands suppression methods of mode-locked fiber laser. The model was based on nonlinear Schrdinger (NLS) equation, nonlinear polarization rotation mode-locking principle and dispersion wave interference theory. The affects of cavity length, gain fiber length and coupling output ratio on the side bands were anelyzed. Mode-locked fiber laser with 0.5 m, 1.5 m and 3 m Er3+-doped fiber (EDF), 13 m, 16 m and 26 m ring length and different output ratios was experimentally studied. Theoretical simulation and experiments show that the EDF length should be appropriately increased to restrain side bands, the ring length should be decreased, the output coupling ratio should be small and the fiber laser should be mode-locked on the fundamental order. The fiber laser with 3 m EDF, 10% ratio and 13 m ring length was experimentally carried out. The output pulse with restrained side bands and spectrum width of 20.4 nm is detected. The repetition rate is 15.87 MHz, and the single pulse energy is 0.52 nJ. The fluctuations of pulse amplitude and spectrum width are 4% and 2%.