The Crank-Nicolson (short for C-N) scheme for solving backward stochastic differential equation (BSDE), driven by Brownian motions, was first developed by the authors W. Zhao, L. Chen and S. Peng [SIAM J. Sci. Comput., 28 (2006), 1563-1581, and numerical experiments showed that the accuracy of this C-N scheme was of second order for solving BSDE. This C-N scheme was extended to solve decoupled forwardbackward stochastic differential equations (FBSDEs) by W. Zhao, Y. Li and Y. Fu [Sci. China. Math., 57 (2014), 665-686], and it was numerically shown that the accuracy of the extended C-N scheme was also of second order. To our best knowledge, among all one-step (two-time level) numerical schemes with second-order accuracy for solving BSDE or FBSDEs, such as the ones in the above two papers and the one developed by the authors D. Crisan and K. Manolarakis [Ann. Appl. Probab., 24, 2 (2014), 652-678], the C-N scheme is the simplest one in applications. The theoretical proofs of second-order error estimates reported in the literature for these schemes for solving decoupled FBSDEs did not include the C-N scheme. The purpose of this work is to theoretically analyze the error estimate of the C-N scheme for solving decoupled FBSDEs. Based on the Taylor and Itô-Taylor expansions, the Malliavin calculus theory (e.g., the multiple Malliavin integration-by-parts formula), and our new truncation error cancelation techniques, we rigorously prove that the strong convergence rate of the C-N scheme is of second order for solving decoupled FBSDEs, which fills the gap between the second-order numerical and theoretical analysis of the C-N scheme.