We have grown GaN layers with in-situ SiN mask by metal organic chemical vapor deposition (MOCVD) and study the physical properties of the GaN layer. We have also fabricate PN junction light emitting diode (LED) to investigate the effect of the SiN mask on its optical property By inserting a SiN mask, (102) the full width at half maximum (FWHM) decreased from 480 arcsec to 409 arcsec and threading dislocation (TD) density decreased from $3.21{ imes}10^9;cm^{-2}$ to $9.7{ imes}10^8;cm^{-2}$. The output power of the LED with a SiN mask increased from 198 mcd to 392 mcd at 20 mA. We have thus shown that the SiN mask improved significantly the physical and optical properties of the GaN layer.