The main objective of this article is to study the nonlinear stability and dynamic transitions of the basic (zonal) shear flows for the three-dimensional continuously stratified rotating Boussinesq model. The model equations are fundamental equations in geophysical fluid dynamics, and dynamics associated with their basic zonal shear flows play a crucial role in understanding many important geophysical fluid dynamical processes, such as the meridional overturning oceanic circulation and the geophysical baroclinic instability. In this paper, first we derive a threshold for the energy stability of the basic shear flow, and obtain a criteria for nonlinear stability in terms of the critical horizontal wavenumbers and the system parameters such as the Froude number, the Rossby number, the Prandtl number and the strength of the shear flow. Next we demonstrate that the system always undergoes a dynamic transition from the basic shear flow to either a spatiotemporal oscillatory pattern or circle of steady states, as the shear strength $\Lambda$ of the basic flow crosses a critical threshold $\Lambda_c$. Also we show that the dynamic transition can be either continuous or catastrophic, and is dictated by the sign of a transition parameter $A$, fully characterizing the nonlinear interactions of different modes. A systematic numerical method is carried out to explore transition in different flow parameter regimes. We find that the system admits only critical eigenmodes with horizontal wave indices $(0,m_y)$. Such modes, horizontally have the pattern consisting of $m_y$-rolls aligned with the x-axis. Furthermore, numerically we encountered continuous transitions to multiple steady states, continuous and catastrophic transitions to spatiotemporal oscillations.