HNTs (halloysite nanotubes) are widely used in reinforcing material, often used in material reinforcement and particle loading. However, their easy agglomeration causes them to have great limitations in application. In this work, two kinds of silane coupling agents (KH560 and KH570) were introduced to graft the CNF/HNT (cellulose nanofiber) nanoparticles used to reinforce the starch-polyvinyl alcohol (PVA) composite membranes. The mechanical properties, water resistance properties and thermal performance of the composite membrane were tested. The results showed that the CNF/HNTs nanoparticle system modified by two silane coupling agents enhanced the tensile strength (TS) of the starch–PVA composite membranes by increments of 60.11% and 68.35%, and, in addition, the water resistance of starch–PVA composite membrane improved. The introduction of chemical bonds formed associations and a compact network structure, which increased the thermal stability and the crystallinity of the starch–PVA composite membrane. In the study, we creatively used CNF to disperse HNTs. CNF and HNTs were combined under the action of the silane coupling agent, and then mixed into the starch–PVA membranes matrix to prepare high-performance degradable biological composite membranes.