Herein, a Monte Carlo ray-tracing method is proposed to investigate the influence of the roughening of the sapphire substrate sidewall caused by laser hidden cutting technology on the light extraction efficiency (LEE) of GaN-based flip chip light-emitting diodes (LEDs). Monte Carlo ray tracing method is used to analyze the influence of the sidewall invisible cutting on the LEE of each light-emitting surface of the LED flip chip and optimize the number and position of the sapphire sidewall invisible cutting of the LED flip chip. Simulation results show that as the number of invisible cutting layers on the sapphire sidewall and equivalent roughness of the sapphire sidewall increase, the LEE of the light-emitting surface on the top of the LED flip chip gradually decreases and the total LEE of the sidewall and LED flip chip gradually increase. The Monte Carlo ray-tracing method is used to simulate the effect of uniform and combined laser dotting on the LEE of the LED flip chip. Experimental results show that when the number of invisible cutting layers is fixed, the sidewalls and total LEE of uniform laser dots are higher than those of combined laser dots.