We propose a self-supervised method for partial point set registration. While recent proposed learning-based methods have achieved impressive registration performance on the full shape observations, these methods mostly suffer from performance degradation when dealing with partial shapes. To bridge the performance gaps between partial point set registration with full point set registration, we proposed to incorporate a shape completion network to benefit the registration process. To achieve this, we design a latent code for each pair of shapes, which can be regarded as a geometric encoding of the target shape. By doing so, our model does need an explicit feature embedding network to learn the feature encodings. More importantly, both our shape completion network and the point set registration network take the shared latent codes as input, which are optimized along with the parameters of two decoder networks in the training process. Therefore, the point set registration process can thus benefit from the joint optimization process of latent codes, which are enforced to represent the information of full shape instead of partial ones. In the inference stage, we fix the network parameter and optimize the latent codes to get the optimal shape completion and registration results. Our proposed method is pure unsupervised and does not need any ground truth supervision. Experiments on the ModelNet40 dataset demonstrate the effectiveness of our model for partial point set registration.