A femtosecond pulse shaper is set up based on a liquid crystal spatial light modulator. The pulse shaper is driven by home-developed LabVIEW programs. The second harmonic generation (SHG) spectrum is recorded when the femtosecond laser pulse is modulated by a sinusoidal phase function. The multi-photon intra-pulse interference phase scan (MIIPS) trace is obtained with the parameter δ, witch is the initial phase of sinusoidal phase scanning, scanning from 0 to 4π. The effects of the sinusoidal phase′s amplitude and frequency (α and γ) are studied in detail for the optimization of MIIPS. The results not only provide a guidance for the phase measurement and compensation in MIIPS, but also supply a method for narrowing and shaping SHG spectrum, which will be useful in many fields, such as two-photon absorption spectroscopy, femtosecond chemistry and femtosecond biology.