The novelty examination of pharmaceutical crystal patents often requires the use of legal presumption as a method of finding out the facts. The process is complex because it involves the allocation and transfer of the burden of proof, the refutation and overturn of the presumed facts, and the use of legal techniques in the investigation of technical facts. Through typical cases, this paper compares the differences among different examination procedures in the judgment of evidence that is sufficient to challenge the novelty of pharmaceutical crystals and shift the burden of proof, and explores the reasons for the differences from the perspectives of the uncertainty of crystal acquisition, the purpose and value of the setting of substantive examination and invalidation procedures, the legal status of patents (applications), the burden of proof and the standard of proof, and further analyze the impacts of the presumption methods of different examination procedures and the performance of the parties' request and rebuttal on the grant and stability of the pharmaceutical crystal patent.