Abstract We investigate, via quantum molecular dynamics simulations, the structural and transport properties of ammonia along the principal Hugoniot for temperatures up to 10 eV and densities up to 2.6 g/cm3. With the analysis of the molecular dynamics trajectories by use of the bond auto-correlation function, we identify three distinct pressure-temperature regions for local chemical structures of ammonia. We derive the diffusivity and viscosity of strong correlated ammonia with high accuracy through fitting the velocity and stress-tensor autocorrelation functions with complex functional form which includes structures and multiple time scales. The statistical error of the transport properties is estimated. It is shown that the diffusivity and viscosity behave in a distinctly different manner at these three regimes and thus present complex features. In the molecular fluid regime, the hydrogen atoms have almost the similar diffusivity as nitrogen and the viscosity is dominated by the kinetic contribution. When entering into the mixture regime, the transport behavior of the system remarkably changes due to the stronger ionic coupling, and the viscosity is determined to decrease gradually and achieve minimum at about 2.0 g/cm3 on the Hugoniot. In the plasma regime, the hydrogen atoms diffuse at least twice as fast as the nitrogen atoms.