As the most prevalent internal modification on eukaryotic mRNAs, N6-methyladenosine (m6A) exists in all plant species so far examined and plays important regulatory roles in various developmental processes. In the model plant Arabidopsis thaliana, those known methyltransferases mainly deposit m6A at their target transcripts near the stop codon or in the 3’ untranslated region. Here, we report that FIONA1 (FIO1), a human METTL16 ortholog, acts as a m6A methyltransferase that determines m6A modifications at over 2000 Arabidopsis transcripts predominantly in the coding region. fio1 loss-of-function mutants show a decrease in global m6A mRNA methylation levels and exhibit an early-flowering phenotype. Nanopore direct RNA sequencing reveals that FIO1 is required for depositing m6A preferentially in the coding sequences of a subset of protein-coding transcripts, which is associated with changes in transcript abundance and alternative polyadenylation. We further find that FIO1-mediated m6A methylation determines the mRNA abundance of a central flowering integrator SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and its upstream regulators, thus preventing premature flowering. Our findings show that FIO1 acts as a unique m6A methyltransferase that mediates m6A modification underlying the floral transition in Arabidopsis.