We develop the theory describing the quantum coupled dynamics of the center-of-mass motion of a nanoparticle and an ensemble of ions co-trapped in a dual-frequency linear Paul trap. We first derive analytical expressions for the motional frequencies and classical trajectories of both nanoparticle and ions. We then derive a quantum master equation for the ion-nanoparticle system and quantify the sympathetic cooling of the nanoparticle motion enabled by its Coulomb coupling to a continuously Doppler-cooled ion. We predict that motional cooling down to sub-kelvin temperatures is achievable in state-of-the-art experiments even in the absence of motional feedback and in the presence of micromotion. We then extend our analysis to an ensemble of N ions, predicting a linear increase of the cooling rate as a function of N and motional cooling of the nanoparticle down to tenths of millikelvin in current experimental platforms. Our work establishes the theoretical toolbox needed to explore the ion-assisted preparation of non-Gaussian motional states of levitated nanoparticles.