Effective representation and reconstruction for human faces are very important in many applications. Existing linear representation methods cannot reconstruct high quality 3D faces with details, while the newest non-linear representation method is less suitable for real shapes since spectral decompositions are unstable across different graphs. To address these problems, we propose a multi-scale graph convolutional autoencoder for face representation and reconstruction. Our autoencoder uses graph convolution, which is easily trained for the data with graph structures and can be used for other deformable models. Our model can also be used for variational training to generate high quality face shapes. Experimental results demonstrate that our model can generate more plausible, complex, and stable 3D shapes, and achieves higher quality face reconstruction compared with state-of-the-art methods.