Nucleate boiling heat transfer (NBHT) from enhanced structures is an effective way to dissipate high heat flux. In the present study, a 3D multi-relaxation-time (MRT) phase-change lattice Boltzmann method in conjunction with conjugated heat transfer treatment is proposed and then applied to the study of cavities behaviours for nucleation on roughened surfaces for an entire ebullition cycle without introducing any artificial disturbance. The bubble departure diameter, departure frequency and total boiling heat transfer rate are also explored. It is demonstrated that the cavity shapes show significant influence on the features of NBHT. The total heat transfer rate increases with the cavity mouth and cavity base area while decreases with the increase in cavity bottom wall thickness. The cavity with low wetting can enhance the heat transfer and improve the bubble release frequency. (C) 2016 Elsevier Ltd. All rights reserved.