Post-transcriptional gene regulatory mechanisms are fundamental to the determination of gene expression dynamics and especially crucial for the earliest stages of animal development in which transcription is nearly silent. Here we performed high-resolution total RNA-sequencing and quantitative mass spectrometry analysis simultaneously on Drosophila maternal-to-zygotic transition (MZT) to reveal the dynamic interchange between transcript and protein expression level at the earliest stage of animal development. Intriguingly, we found that both stable transcript expression and an increase in translation efficiency can be crucial for protein upregulation prior to zygotic gene activation (ZGA), whereas such features diminished following ZGA. Further, this study is the first to report the proteome-wide quantitative changes in protein ubiquitination in Drosophila MZT. Our results indicate that timely ubiquitination of the distinct target proteins during MZT are essential for the downregulation of protein expression levels. Profiling of the RNA-associated proteome changes in Drosophila MZT suggested that RNA-binding activities can be regulated without the respective change in net protein expression levels for over 200 proteins, including Pcid2, Sym, and Cpsf73. Taken together, we find that stable expression of transcript can be crucial for the protein expression level upregulation during the earliest stage of MZT, and also report that proteome wide and quantitative remodeling of the distinct post translational regulatory mechanisms can be crucial for the gene expression level changes and progression of the earliest stages of animal development.