Integrating spheres are often used to measure the total luminous flux of lamps by comparison methods, including power-spectral method and photometric method. Correction factors are introduced to compensate the loss of luminous flux due to self-absorption effect in the measurement process with the two methods. Difference in self-absorption effect compensation between the power-spectral method and the photometric method in luminous flux measurement is studied. According to the fundamental principle of luminous flux measurement, the expressions of modified luminous flux are obtained. Based on experimental data and theoretical analysis, influence of auxiliary lamps with different spectra on luminous flux results measured by the two methods is discussed. The results show that modified luminous flux is irrelevant to the relative power distribution of auxiliary lamps by the power-spectral method instead of that by the photometric method. Further results indicate that the modified luminous flux obtained by the power-spectral method remains same in spite of auxiliary lamps with different spectra, however, the modified value of luminous flux changes when the photometric method is used.