Abstract: In multilingual pre-training with the objective of MLM (masked language modeling) on multiple monolingual corpora, multilingual models only learn cross-linguality implicitly from isomorphic spaces formed by overlapping different language spaces due to the lack of explicit cross-lingual forward pass. In this work, we present CLPM (Cross-lingual Prototype Masking), a dynamic and token-wise masking scheme, for multilingual pre-training, using a special token $[\mathcal{C}]_{x}$ to replace a random token $x$ in the input sentence. $[\mathcal{C}]_{x}$ is a cross-lingual prototype for $x$ and then forms an explicit cross-lingual forward pass. We instantiate CLPM for the multilingual pre-training phase of UNMT (unsupervised neural machine translation), and experiments show that CLPM can consistently improve the performance of UNMT models on $\{De, Ro, Ne \} \leftrightarrow En$. Beyond UNMT or bilingual tasks, we show that CLPM can consistently improve the performance of multilingual models on cross-lingual classification.