The invention discloses an enhanced negatively-charged fluorine-containing polymer-based composite membrane based on the interlayer covalent effect. The composite membrane consists of a supporting layer and a functional layer, wherein the supporting layer is an enhancement layer containing polyester fibers, the functional layer consists of a fluorine-containing polymer and a negatively-charged polymer, and the mass percentage content of the negatively-charged polymer is 5-40% of the functional layer. The supporting layer and the functional layer in the composite membrane are combined through the effect of C-O and/or C-N covalent bonds, the composite membrane is a negatively-charged microfiltration membrane or ultrafiltration membrane, and the surface of the composite membrane comprises carboxyl groups and/or sulfonic groups. The composite membrane provided by the invention has the characteristics of high flux, good flux stability, excellent interception and stain resistance, stable binding stability among layers in the membrane, and the like. At the same time, the membrane is negatively charged, and thus the composite membrane has better selectivity and stain resistance to certaincharged pollutants. Therefore, the membrane has stable comprehensive performance, long membrane service life and backwashing durability in the use process. The invention also discloses a preparation method of the composite membrane, and the production process is simple, and is suitable for preparing a flat film or a hollow fiber membrane.