BESIII experiment has collected $e^+e^-$ collision data samples corresponding to integrated lumonisities of 2.93~fb$^{-1}$, 3.19~fb$^{-1}$ and 3.13~fb$^{-1}$ at the center-of-mass~(c.m.) energies of 3.773~GeV, 4.178~GeV, and 4.189-4.226~GeV, respectively. We report the measurements of strong phase differences in $D^0$ decays, including $K_{S/L}^0\pi^+\pi^-$, $K_{S/L}^0K^+K^-$, $K^+\pi^-\pi^-\pi^+$ and $K^-\pi^+\pi^0$, which can reduce the systematic uncertainty of $\gamma/\phi_3$ measurement at LHCb and Belle II experiments. In addition, we report the amplitude analyses and measurements of the absolute branching fractions of $D^0$, $D^+$ and $D_s$ decays.