In this paper, we address the message-passing receiver design for the 3D massive MIMO-OFDM systems. With the aid of the central limit argument and Taylor-series approximation, a computationally efficient receiver that performs joint channel estimation and decoding is devised by the framework of expectation propagation. Specially, the local belief defined at the channel transition function is expanded up to the second order with Wirtinger calculus, to transform the messages sent by the channel transition function to a tractable form. As a result, the channel impulse response (CIR) between each pair of antennas is estimated by Gaussian message passing. In addition, a variational expectation-maximization (EM)-based method is derived to learn the channel power-delay-profile (PDP). The proposed joint Jianhua Lu is with the Department of Electronic Engineering, Tsinghua University, China (e-mail: lhh-dee@mail.tsinghua.edu.cn). 2 algorithm is assessed in 3D massive MIMO systems with spatially correlated channels, and the empirical results corroborate its superiority in terms of performance and complexity.