The high single fundamental mode output power vertical cavity surface emitting laser (VCSEL) has been attracted many attention due to its important applications in the fields of optical communications, sensing, atomic frequency standard and opto-electronic hybrid integration. With suitable photonic crystal structure and distribution, the lateral modes of VCSEL can be effectively controlled by introducing the photonic crystal structure into the top distribution Bragg reflector (DBR). In this paper, square array photonic crystal structure was introduced into the VCSEL to control the transverse mode and single fundamental mode output power. The plane wave expansion and the full-vector three-dimensional finite difference time domain method (FDTD) method were used to analyze the photonic crystal structure and arrangement. The important parameters such as the period, the duty cycle and the etching depth of the square arrangement photonic crystal were obtained by using these methods. The high output power square lattice photonic crystal single fundamental mode VCSEL was reported. The single fundamental mode output power of the square lattice photonic crystal VCSEL is larger than 3 mW and the side mode suppression ratios (SMSRs) is more than 40 dB.