We investigate the cosmological perturbation theory and calculate the perturbation spectra in the warm $k$-inflation. Unlike the scalar perturbations of $k$-inflation in the cold inflationary scenario, entropy perturbations should be considered in our model. We study how the entropy perturbations affect the evolution of curvature perturbation $\mathcal{R}$ on the comoving hypersurfaces and find the dissipation coefficient $\Gamma$ plays a central role in the entropy perturbations and the evolution equation of $\mathcal{R}$. In the weak dissipation condition, entropy perturbations on the large scale can be neglected such that the primordial spectrum of cosmological perturbations is due only to adiabatic perturbations. Like general warm inflationary models, density fluctuations also mainly originated from the thermal fluctuations of the inflaton field rather than the vacuum fluctuations in our model. Finally, we calculate the perturbation spectra and the tensor-to-scalar ratio, then find the tensor-to-scalar ratio is smaller than that in the $k$-inflation or the general potential-driven cold inflationary models.