Titanium dioxide (TiO2) is an excellent candidate material for semiconductor metal oxide-based substrates for surface-enhanced Raman scattering (SERS). Biotemplated fabrication of TiO2 thin films with a 3D network is a promising route for effectively transferring the morphology and ordering of the template into the TiO2 layer. The control over the crystallinity of TiO2 remains a challenge due to the low thermal stability of biopolymers. Here is reported a novel strategy of the cellulose nanofibril (CNF)-directed assembly of TiO2/CNF thin films with tailored morphology and crystallinity as SERS substrates. Polymorphous TiO2/CNF thin films with well-defined morphology are obtained by combining atomic layer deposition and thermal annealing. A high enhancement factor of 1.79 × 106 in terms of semiconductor metal oxide nanomaterial (SMON)-based SERS substrates is obtained from the annealed TiO2/CNF thin films with a TiO2 layer thickness of 10 nm fabricated on indium tin oxide (ITO), when probed by 4-mercaptobenzoic acid molecules. Common SERS probes down to 10 nm can be detected on these TiO2/CNF substrates, indicating superior sensitivity of TiO2/CNF thin films among SMON SERS substrates. This improvement in SERS sensitivity is realized through a cooperative modulation of the template morphology of the CNF network and the crystalline state of TiO2.