In this paper we solve the eigenvalue problem of stochastic Hamiltonian system with boundary conditions. Firstly, we extend the results in Peng [12] from time-invariant case to time-dependent case, proving the existence of a series of eigenvalues $ \{\lambda_m\} $ and construct corresponding eigenfunctions. Moreover, the order of growth for these $ \{\lambda_m\} $ are obtained: $ \lambda_m\sim m^2 $, as $ m\rightarrow +\infty $. As applications, we give an explicit estimation formula about the statistic period of solutions of Forward-Backward SDEs. Besides, by a meticulous example we show the subtle situation in time-dependent case that some eigenvalues appear when the solution of the associated Riccati equation does not blow-up, which does not happen in time-invariant case.
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