We study here the spectral characteristics of square-wave-modulated type II long-period fiber gratings (LPFGs) inscribed by a femtosecond laser. Both theoretical and experimental results indicate that higher-order harmonics refractive index (RI) modulation commonly exists together with the fundamental harmonic RI modulation in such LPFGs, and the duty cycle of a square wave has a great influence on the number and amplitudes of higher-order harmonics. A linear increase in the duty cycle in a series of square wave pulses will induce another LPFG with a minor difference in periods, which is useful for expanding the bandwidth of LPFGs. We also propose a method to reduce insertion loss by fabricating type II LPFGs without higher-order harmonic resonances. This work intensifies our comprehension of type II fiber gratings with which novel optical fiber sensors can be fabricated.