A InGaN/GaN micro-square array light-emitting diode (LED) chip (micro-chip) has been successfully fabricated by the focused ion beam (FIB) etching technique, which can reduce ohmic contact degradation in the fabrication process of three-dimensional (3D) structure devices. Our results show that the micro-chip exhibits a similar current–voltage performance compared to the corresponding InGaN/GaN planar LED chip (planar-chip). At the driving current of 20 mA, the output power of the micro-chip is improved by 17.8% in comparison to that of the planar-chip. A relatively broad emission and enhanced emission intensity in the perpendicular direction are obtained in angular-resolved EL (AREL) measurements for the micro-chip. Three-dimensional finite difference time domain (FDTD) simulations have also proven enhanced emitted optical energy distribution. The enhancement mechanism is correlated to the increased light extraction efficiency (LEE) of the micro-chip, mainly owing to more photons from the exposed MQWs surfaces that can be efficiently extracted by the micro-square array.