Errors are introduced when using traditional methods for measuring the total luminous flux of LEDs since an LED is quite different from traditional light sources in terms of physical size, flux level, spectrum and spatial distribution. This paper uses commercial lighting simulation software named Tracepro to simulate the self-absorption effect when using traditional integrating sphere methods to measure the total luminous flux of LEDs and then presents a modified method for the measurement. The LED under investigation or a specially designed narrow beam standard lamp is placed on the interior wall of the sphere in our method. The results show that the measurement method presented here can lead to better precision in the evaluation of the total luminous flux of LEDs.