By analyzing $2.93\ \rm fb^{-1}$ of data taken at the $\psi(3770)$ resonance peak with the BESIII detector, we measure the branching fractions for the hadronic decays $D^+\to K^0_SK^0_S K^+$, $D^+\to K^0_SK^0_S \pi^+$, $D^0\to K^0_S K^0_S$ and $D^0\to K^0_SK^0_SK^0_S$. They are determined to be ${\mathcal B}(D^+\to K^0_SK^0_SK^+)=(2.54 \pm 0.05_{\rm stat.} \pm 0.12_{\rm sys.})\times 10^{-3}$, ${\mathcal B}(D^+\to K^0_SK^0_S\pi^+)=(2.70 \pm 0.05_{\rm stat.} \pm 0.12_{\rm sys.})\times 10^{-3}$, ${\mathcal B}(D^0\to K^0_SK^0_S)=(1.67 \pm 0.11_{\rm stat.} \pm 0.11_{\rm sys.})\times 10^{-4}$ and ${\mathcal B}(D^0\to K^0_SK^0_SK^0_S)=(7.21 \pm 0.33_{\rm stat.} \pm 0.44_{\rm sys.})\times 10^{-4}$, where the second one is measured for the first time and the others are measured with significantly improved precision over the previous measurements.