Superhydrophobic nanocellulose membrane was prepared by synergistically modifying biodegradable nanocellulose with low-carbon perfluoroorganosiloxane and ethyl orthosilicate. The effects of four kinds of low-carbon perfluoroorganosiloxanes with different structures and their ratio to ethyl orthosilicate on the hydrophobic properties of nanocellulose membrane were investigated, and then FT-IR, XPS, XRD, SEM, TEM, AFM, TG and contact angle goniometer were used to characterize the structure and hydrophobic properties of nanocellulose membrane before and after modification. It is found that when the molar ratio of 1H,1H,2H,2H-perfluorooctyltrimethoxysilane (PFOTMS) to ethyl orthosilicate (TEOS) is 1, the modified nanocellulose membrane PFOTMS-TEOS-CNF is loaded with silica nanoparticles both inside and on its surface, and a micro-nano hierarchical rough morphology with low surface energy is constructed. At this point, the root-mean-square roughness (Rq) of nanocellulose membrane is 112 nm, and the static contact angle of water droplet is 153.5°, successfully realizing superhydrophobicity. In addition, compared to unmodified nanocellulose membrane, PFOTMS-TEOS-CNF with better thermal stability includes an additional maximum weight loss rate temperature (491.2 °C). The above advantages markedly improve the shortcomings of pristine nanocellulose, such as superhydrophilicity and insufficient thermal stability, and also broadens its high-value application in many fields.