With the development of nanotechnology, nanomaterials have been introduced to improve the engineering properties of cement-based building materials. An abundant number of studies have been carried out on normal-weight concrete using multi-walled carbon nanotubes (MWCNTs) or nano-silica (NS) and have proven their effectiveness. Nevertheless, still very few investigations are available in terms of lightweight cement-based materials, especially when MWCNTs and NS are binarily incorporated. Thus, in this study, fly ash cenospheres (FACs) according to cement weight were applied as lightweight fine aggregates to produce lightweight mortar (LWM). MWCNTs at 0.05, 0.15, and 0.45% and NS at 0.2 and 1.0% were binarily added as modifiers. Compressive and flexural strengths were tested to investigate mechanical behaviors. A water absorption test was conducted, together with scanning electron microscopy (SEM) and mercury intrusion porosimetry (MIP), to identify the impacts of the nano-additives on the pore structure of LWM. The following results were obtained: MWCNTs and NS demonstrated synergic effects on enhancing the mechanical properties of LWM. MWCNTs exerted positive impacts on reducing the porosity and improving the pore distribution at low dosages of 0.05 and 0.15%. The hybrid addition of NS further transformed large voids into small ones and introduced closed pores.