Natural aquifer heterogeneity controls the groundwater flow and solute transport, and how to accurately quantify the flow and solute transport in heterogeneous aquifers has received wide attention by many scholars, and has become a hot research topic in earth science. Theoretically, a systematic review is given by the following aspect: flow and solute transport model, moment analysis, multiscale analysis. The resolved and remained issues for scale conversion in hydrogeology research are pointed out. Secondly, recent advances of heterogeneous field test, uncertainty and velocity connectivity are analyzed. Finally, the geophysical inversion of aquifer heterogeneity, stochastic theory and development of stochastic simulation software, scale conversion and uncertainty of velocity connectivity, and the relationship between heterogeneity and hydrogeological condition on the major four aspects of the future research direction is pointed out.