Using the data sample of an integrated luminosity of 2.93 fb$^{-1}$ taken at the center-of-mass energy of 3.773 GeV, we search for the Majorana neutrino in the lepton number violating decays $Dto K pi e^+ e^+$. No significant signal is observed, and the upper limits on the branching fraction at the 90% confidence level are set to be $mathcal{B},(D^0 to K^- pi^- e^+ e^+)<2.8times10^{-6}$, $mathcal{B},(D^+ to K_S^0 pi^- e^+ e^+)<3.3times10^{-6}$ and $mathcal{B},(D^+ to K^- pi^0 e^+ e^+)<8.5times10^{-6}$. The Majorana neutrino is searched for with different mass assumptions ranging from 0.25 to 1.0 GeV/$c^2$ in the decays $D^0to K^- e^+ u_N(pi^- e^+)$ and $D^+to K_S^0 e^+ u_N(pi^- e^+)$, and the upper limits on the branching fraction at the 90% confidence level are extracted to be at the level of $10^{-7} sim 10^{-6}$, depending on the mass of Majorana neutrino. The constraints on the mixing matrix element $|V_{eN}|^2$ are also evaluated.