N-methyladenosine (mA) and its regulatory components play critical roles in various developmental processes in mammals. However, the landscape and function of mA in early embryos remain unclear owing to limited materials. Here we developed a method of ultralow-input mA RNA immunoprecipitation followed by sequencing to reveal the transcriptome-wide mA landscape in mouse oocytes and early embryos and found unique enrichment and dynamics of mA RNA modifications on maternal and zygotic RNAs, including the transcripts of transposable elements MTA and MERVL. Notably, we found that the maternal protein KIAA1429, a component of the mA methyltransferase complex, was essential for mA deposition on maternal mRNAs that undergo decay after zygotic genome activation and MTA transcripts to maintain their stability in oocytes. Interestingly, mA methyltransferases, especially METTL3, deposited mA on mRNAs transcribed during zygotic genome activation and ensured their decay after the two-cell stage, including Zscan4 and MERVL. Together, our findings uncover the essential functions of mA in specific contexts during the maternal-to-zygotic transition, namely ensuring the stability of mRNAs in oocytes and the decay of two-cell-specific transcripts after fertilization.