We study a light dark matter in a radiative neutrino model to explain the X-ray line signal at about $3.5$ keV recently reported by XMN-Newton X-ray observatory using data of various galaxy clusters and Andromeda galaxy. The signal requires very tiny mixing between the dark matter and an active neutrino; $sin^2 2thetaapprox 10^{-10}$. It could suggest that such a light dark matter cannot contribute to the observed neutrino masses if we use the seesaw mechanism. In other words, neutrino masses might come a structure different from the dark matter. We propose a model in which Dirac type active neutrino masses are induced at one-loop level. On the other hand the mixing between active neutrino and dark matter are generated at two-loop level. As a result we can explain both the observed neutrino masses and the X-ray line signal from the dark matter decay with rather mild hierarchy of parameters in TeV scale.