We study perturbations of a scalar field cosmology in Horava-Lifshitz gravity, adopting the most general setup without detailed balance but with the projectability condition. We derive the generalized Klein-Gordon equation, which is sixth-order in spatial derivatives. Then we investigate scalar field perturbations coupled to gravity in a flat Friedmann-Robertson-Walker background. In the sub-horizon regime, the metric and scalar field modes have independent oscillations with different frequencies and phases except in particular cases. On super-horizon scales, the perturbations become adiabatic during slow-roll inflation driven by a single field, and the comoving curvature perturbation is constant.