Some related research of intergenerational mobility concludes that "higher-level intergenerational mobility results in lower-degree inequality", but this does not seem to be consistent with China's reality completely. The possible reasons lie in that traditional intergenerational mobility research does not distinguish between long-run and short-run values effectively, and also does not take the uncertainty of human capital formation into account. In view of these problems, this paper constructs an overlapping generations model and makes a comparative analysis of intergenerational mobility in public education system and market education system. Accordingly, it comes to the conclusions as follows:firstly, long-run inequality in public education system is always lower than one in market education system; secondly, the increase in short-term, intergenerational mobility is not always accompanied by inequality, and when the society is subject to some intensive shocks, the same increase or decrease in these two may occur; thirdly, radical education system reform leads to sharp rise in convergence rate of human capital and the increase in short-term and long-term in equality, and the intergenerational mobility constantly converges to new and lower steady-state value after sudden drop; fourthly, the parameter value of the uncertainty of human capital accumulation reflects unpredicable skills or innate endowments of individuals, and is an important factor affecting interfeneratonal mobility and in equality; the sudden rise in uncertainty leads to the sharp increase in short-run inequality & a new high level of long-term inequality, and rapid rise in short-run intergenerational mobility, but its steady-state value remains constant. These conclusions are beneficial to the clarification of the complex relationship between intergenerational mobility and inequality, and also can provide reference for relevant empirical research.