In many engineering networks, only a part of target state variables are required to be estimated. On the other hand, multi-layer complex network exists widely in practical situations. In this paper, the state estimation of target state variables in multi-layer complex dynamical networks with nonlinear node dynamics is studied. A suitable functional state observer is constructed with the limited measurement. The parameters of the designed functional observer are obtained from the algebraic method and the stability of the functional observer is proven by the Lyapunov theorem. Some necessary conditions that need to be satisfied for the design of the functional state observer are obtained. Different from previous studies, in the multi-layer complex dynamical network with nonlinear node dynamics, the proposed method can estimate the state of target variables on some layers directly instead of estimating all the individual states. Thus, it can greatly reduce the placement of observers and computational cost. Numerical simulations with the three-layer complex dynamical network composed of three-dimensional nonlinear dynamical nodes are developed to verify the effectiveness of the method.