Based on the dynamic monitoring data of floating population in 2015，this study adopts the quantile regression and quantile decomposition analysis to explore the wage difference between the rural and urban floating population．There is a significant income gap between the groups of the floating population．In addition to the characteristic differences，discrimination resulting from the household registration system stands at as high as 36．8% of the total impact on wage income difference．Meanwhile，the coefficients affecting the income at different quantiles significantly differ between the rural and urban floating population．In the counterfactual state，increase of the income quantile ( income level) leads to widening of the income gap of the two groups，and the impact of the discrimination deepens， which is as high as 75．1% in 90% quantile．Apparently，reforming the household registration system will help narrow the income gap within the floating population．Furthermore，a range of supporting policies are needed to reduce the discrimination and to promote urban-rural integration．