Soil salinization is a major abiotic stress limiting wheat production. Although transcriptional responses to salt stress are well-studied, the role of post-transcriptional regulation, particularly through RNA modifications, remains unclear in wheat (Triticum aestivum L.). Here, we present an integrated analysis of the early salt stress response using Nanopore direct RNA sequencing (DRS) and quantitative proteomics. We generated genome-wide maps of N6-methyladenosine (m6A) modifications, concurrently profiling alternative polyadenylation (APA) events and poly(A) tail length (PAL) dynamics. This multi-omics approach characterizes coordinated epitranscriptomic reprogramming and enabled the construction of a regulatory network linking m6A marks to proteomic changes. Furthermore, we identified and functionally validated the putative m6A reader protein TaECT5 as a positive regulator of wheat salt tolerance. Our study provides a systems-level view of post-transcriptional regulation during salt stress in wheat and identifies potential targets for enhancing salt tolerance.