This work investigates the effect of three-dimensional joint roughness coefficient ( $\mathit{JRC}^{3D}$ ) on the nonlinear shear creep properties of granite structural planes. Four natural granite structural planes with distinct surface morphologies were prepared using the Brazilian splitting method, with $\mathit{JRC}^{3D}$ values controlled within the typical engineering range of 5-18. A self-developed laser three-dimensional scanner was employed to capture surface morphology, enabling three-dimensional visualization and quantification of morphological parameters. Shear creep tests were then conducted to examine the effect of $\mathit{JRC}^{3D}$ on the creep behavior of the structural planes. The results show that with increasing $\mathit{JRC}^{3D}$ , creep deformation, steady-state creep rate, and accelerated creep rate gradually decrease, whereas failure shear stress, creep failure time, and long-term shear strength exhibit an increasing trend. Based on these findings, a shear creep model incorporating the influence of $\mathit{JRC}^{3D}$ was developed. Model parameters were identified and validated, confirming the model’s reliability. The model quantitatively links $\mathit{JRC}^{3D}$ to creep parameters of engineering rock joints, addressing limitations of traditional models that neglect surface morphology effects. By capturing the progressive damage evolution in rock masses, the model provides a mechanistic framework for predicting time-dependent instability and mitigating the risk of abrupt collapses induced by creep accumulation. These results offer valuable guidance for the prevention, control, and evaluation of geological engineering hazards.