Dynamic RNA-protein interactions influence RNA transport, storage, stability, and activity, and are fundamental to a broad range of biological processes. During the oocyte-to-embryo (OET) transition, in which fully differentiated cells regain totipotency, tens of thousands of maternal transcripts deposited in the oocyte interact with protein complexes in a tightly regulated manner, enabling precise spatiotemporal regulation of gene expression required for meiotic oocyte maturation, fertilization, egg activation, mitotic cell division, and zygotic genome activation. Despite their critical importance, the dynamics of RNA-protein interaction during the OET remain poorly understood. Here, we leverage fractionation RNA-seq to profile RNA insolubility dynamics, a proxy for RNA-protein interaction, during zebrafish OET. We identify transcripts that transition between soluble (relatively free) and insoluble (heavily protein-associated) states and demonstrate that these phase transitions are driven by both ribosome-dependent and ribosome-independent mechanisms. Notably, ribosome-independent phase transitions represent an important layer of translational regulation that fine-tunes the expression of maternal transcripts. We provide evidence that the capacity of maternal RNAs to engage with protein complexes changes dynamically during the OET. Further analyses reveal that both poly(A) tail dynamics and m6A modifications of RNA play key roles in regulating RNA solubility phase transitions during the OET. By leveraging machine learning, we found that the RNA solubility phase transition is regulated by an interplay among static sequence-specific cis-elements, dynamic RNA features, and transacting factors. Together, our findings uncover multilayered cis-regulatory mechanisms that shape dynamic RNA–protein interactions during the OET, providing fundamental insights into post-transcriptional gene regulation during early development.