A series of aliphatic waterborne polyurethane (WPU) dispersions with high ionic concentration were synthesized by prepolymer mixing. The resultant structure property relationships were investigated. It was revealed that there was a new microphase besides the phase separation between the soft and the hard domains. The new microphase separation found in the hard domains was formed by aggregation of the ionic groups characterized by dynamic mechanical analysis, FTIR characterization, and thermal gravimetric analysis.