FreeFlow-ONT is a user-friendly and modular platform designed for reference genome-free m6A analysis of ONT direct RNA sequencing (DRS) data. It aims to support streamlined, end-to-end analysis under conditions where high-quality reference genomes or annotations are unavailable. By integrating long-read transcriptome assembly, m6A modification identification, differential modification analysis, and machine learning-based prediction into a unified Galaxy environment, FreeFlow-ONT enables reproducible and flexible analysis of plant m6A data from raw signals to biologically interpretable results. FreeFlow-ONT comprises eight functional modules: Data Preparation, Quality Control, Transcriptome Construction, Transcriptome Evaluation, RNA Modification Identification, Functional Annotation, Differential Modification Analysis, and Machine Learning-based Prediction.