Dentin is a natural composite material consisting of three phases: mineral, organic and water. These three phases are not independent each other, but rather work in harmony to determine the viscoelastic property of dentin. Although the viscoelastic properties of root dentin at a macroscopic level have been studied, those of the crown to root dentin at a microscopic level have not. Dynamic nanoindentation is a new promising method of measuring the dynamic viscoelastic properties of biological tissues with a smaller length and using smaller load scales than those allowed by other testing methods. The objective of the present study was to use the dynamic nanoindentation method to determine dynamic viscoelastic properties such as storage modulus and loss tangent of human crown to root dentin at the microscopic level in a tooth direction. The effects of dentin mineral density (DMD) measured by pQCT on viscoelastic properties at a macroscopic level were also studied. The DMD at the crown dentin was higher than that at the root dentin. The storage modulus of crown dentin was higher than that of root dentin, however the loss tangent of crown dentin was lower than that of root dentin. It was found that a positive correlation existed between the storage modulus and DMD (r = 0.72). The loss tangent was negatively correlated with DMD (r = - 0.23).