The propagation of three-dimensional nonlinear dust-acoustic and dust-Coulomb waves in unmagnetized/magnetized dusty plasmas consisting of electrons, ions, and charged dust particles is investigated. The grain charge fluctuation effect is also incorporated through the current balance equation. By using the perturbation method,a Kadomtsev-Petviashvili equation and a Zakharov-Kuznetsov equation governing the nonlinear waves in the unmagnetized and magnetized systems are obtained respectively. It has been shown that with the combined effects of grain charge fluctuation, the transverse perturbation, and the external magnetic field would modify the wave structures.Waves in those systems are unstable to the high-order long-wave perturbations.