Geometric structures of dynamical systems are investigated based on a differential geometric method (Jacobi stability of KCC-theory). This study focuses on differences of Jacobi stability of two-dimensional second-order differential equation from that of one-dimensional second-order differential equation. One of different properties from a one-dimensional case is the Jacobi unstable condition given by eigenvalues of deviation curvature with different signs. Then, this geometric theory is applied to an overhead crane system as a two-dimensional dynamical system. It is shown a relationship between the Hopf bifurcation of linearized overhead crane and the Jacobi stability. Especially, the Jacobi stable trajectory is found for stable and unstable spirals of the two-dimensional linearized system. In case of the linearized overhead crane system, the Jacobi stable spiral approaches to the equilibrium point faster than the Jacobi unstable spiral. This means that the Jacobi stability is related to the resilience of deviated trajectory in the transient state. Moreover, for the nonlinear overhead crane system, the Jacobi stability for limit cycle changes stable and unstable over time.