Three-dimensional topological gapless matters with gapless degeneracies protected by a topological invariant defined over a closed manifold in momentum space have attracted considerable interest in various fields ranging from condensed matter materials to ultracold atomic gases. As a highly controllable and disorder free system, ultracold atomic gases provide a versatile platform to simulate topological gapless matters. Here, the current progress in studies of topological gapless phenomena in three-dimensional cold atom systems is summarized in the review. It is mainly focused on Weyl points, structured (type-II) Weyl points, Dirac points, nodal rings and Weyl exceptional rings in cold atoms. Since interactions in cold atoms can be controlled via Feshbach resonances, the progress in both superfluids for attractive interactions and non-interacting cold atom gases is reviewed.