Using a data sample of $e^+e^-$ collision data with an integrated luminosity of 2.93 fb$^{-1}$ taken at the center-of-mass energy $\sqrt s= 3.773$~GeV with the BESIII detector operating at the BEPCII storage rings, we measure the absolute branching fractions of the two-body hadronic decays $D^+\to \pi^+\pi^0$, $K^+ \pi^0$, $\pi^+ \eta$, $K^+\eta$, $\pi^+\eta^\prime$, $K^+\eta^\prime$, $K_S^0 \pi^+$, $K_S^0 K^+$, and $D^0\to \pi^+ \pi^-$, $K^+ K^-$, $K^\mp \pi^\pm$, $K_S^0 \pi^0$, $K_S^0 \eta$, $K_S^0 \eta^\prime$. Our results are consistent with previous measurements within uncertainties. Among them, the branching fractions for $D^+\to\pi^+\pi^0$, $K^+\pi^0$, $\pi^+\eta$, $\pi^+\eta^\prime$, $K_S^0 \pi^+$, $K_S^0 K^+$ and $D^0 \to K_S^0 \pi^0$, $K_S^0 \eta$, $K_S^0 \eta^\prime$ are determined with improved precision compared to the world average values.