Irregular-shaped and partially degraded secondary microplastics (SMP) account for the majority of MPs in marine environments, yet little is known about their effects on marine organisms. In this study, we investigated the embryotoxicity of polyvinyl chloride SMP and primary microplastics (PMP) to the marine medaka Oryzias melastigma. This study aimed to determine the physical impacts of MPs and, for the first time, elucidate the underlying mechanisms of physical toxicity. SMP shortened hatching time and induced higher teratogenic effects on larvae relative to PMP, indicating a higher toxicity from SMP. Physical damage from SMP to the chorion surface appears to be the main toxicity mechanism, caused by their irregular shape and reduced aggregation relative to PMP. In contrast, real-time changes in oxygen demonstrated that hypoxia caused by greater PMP adsorption to the chorion surface contributes to the toxicological responses of this material relative to SMP. Modulation of genes involved in hypoxia-response, cardiac development and hatching confirmed the toxicity mechanisms of PMP and SMP. The chemical contribution to observed toxicity was negligible, confirming impacts derived from physical toxicity. Our findings highlight the negative effects of environmentally relevant SMP on the marine ecosystems.