The success of existing multi-view clustering relies on the assumption of sample integrity across multiple views. However, in real-world scenarios, samples of multi-view are partially available due to data corruption or sensor failure, which leads to incomplete multi-view clustering study (IMVC). Although several attempts have been proposed to address IMVC, they suffer from the following drawbacks: i) Existing methods mainly adopt cross-view contrastive learning forcing the representations of each sample across views to be exactly the same, which might ignore view discrepancy and flexibility in representations; ii) Due to the absence of non-observed samples across multiple views, the obtained prototypes of clusters might be unaligned and biased, leading to incorrect fusion. To address the above issues, we propose a Cross-view Partial Sample and Prototype Alignment Network (CPSPAN) for Deep Incomplete Multi-view Clustering. Firstly, unlike existing contrastive-based methods, we adopt pair-observed data alignment as ‘proxy supervised signals’ to guide instance-to-instance correspondence construction among views. Then, regarding of the shifted prototypes in IMVC, we further propose a prototype alignment module to achieve incomplete distribution calibration across views. Extensive experimental results showcase the effectiveness of our proposed modules, attaining noteworthy performance improvements when compared to existing IMVC competitors on benchmark datasets.