Physical-layer key generation (PKG) in multi-user massive MIMO networks faces great challenges due to the large length of pilots and the high dimension of channel matrix. To tackle these problems, we propose a novel massive MIMO key generation scheme with pilot reuse based on the beam domain channel model and derive close-form expression of secret key rate. Specifically, we present two algorithms, i.e., beam-domain based channel probing (BCP) algorithm and interference neutralization based multi-user beam allocation (IMBA) algorithm for the purpose of channel dimension reduction and multi-user pilot reuse, respectively. Numerical results verify that the proposed PKG scheme can achieve the secret key rate that approximates the perfect case, and significantly reduce the dimension of the channel estimation and pilot overhead.