Canonical correlation analysis (CCA) is a statistical analysis tool for analyzing the correlation between two sets of random variables. CCA requires the data be rigorously paired or one-to-one correspondence among different views due to its correlation definition. However, such requirement is usually not satisfied in real-world applications due to various reasons. Often, only a few paired and a lot of unpaired multi-view data are given, because unpaired multi-view data are relatively easier to be collected and pairing them is difficult, time consuming and even expensive. Such data is referred as semi-paired multi-view data. When facing semi-paired multi-view data, CCA usually performs poorly. To tackle this problem, a semi-paired variant of CCA, named SemiPCCA, is proposed based on the probabilistic model for CCA. The actual meaning of "semi-" in SemiPCCA is "semi-paired" rather than "semi-supervised" as in popular semi-supervised learning literature. The estimation of SemiPCCA model parameters is affected by the unpaired multi-view data which reveal the global structure within each modality. By using artificially generated semi-paired multi-view data sets, the experiment shows that SemiPCCA effectively overcome the over-fitting problem of traditional CCA and PCCA (probabilistic CCA) under the condition of insufficient paired multi-view data and performs better than the original CCA and PCCA. In addition, an automatic image annotation method based on the SemiPCCA is presented. Through estimating the relevance between images and words by using the labelled and unlabeled images together, this method is shown to be more accurate than previous published methods.