Micro-scale light emitting diodes (micro-LEDs) commonly employ a thin-film flip-chip (TFFC) structure whose substrate is lifted off by an excimer laser. However, flip-chip (FC) micro-LEDs with a substrate can provide a sharp rise on sidewall emission by increasing the sidewall area. Here, we investigate the influence of substrate thickness, encapsulation, surface texture, microstructures between the substrate and epilayer, as well as the size, cutting shape, and angle of the chip on the light extraction efficiencies (LEEs) of FC micro-LEDs by using the Monte Carlo ray tracing method. We find that the LEE of the blue FC micro-LED chip increases by 46.5% over that of the blue TFFC micro-LED chip. After the encapsulation with the epoxy lens is applied, the LEEs of the blue TFFC micro-LED and blue FC micro-LED increase by 129% and 110.5%, respectively. The underlying mechanisms for the use of surface texture, patterned sapphire substrate, air-void array, and chip shaping technologies to improve the LEEs of FC micro-LEDs are also investigated in detail. We find that the LEEs AlGaInP based red FC micro-LED and GaN based blue/green FC micro-LEDs exhibit a sharp rise when the chip size drops from 30 to 10 µm. The inverted trapezoid FC micro-LED with patterned sapphire substrate (PSS) and encapsulation shows extraordinarily strong top emission and high collimation. We believe that our study offers a promising and practical route for obtaining high efficiency micro-LEDs.