The invention discloses a silk protein-based flexible composite sensor and a preparation method thereof, the flexible composite sensor comprises a flexible substrate, an interdigital electrode and a composite sensing material, the flexible substrate can be directly attached to the skin or the surface of other detected objects, the interdigital electrode is located between the flexible substrate and the composite sensing material, the composite sensing material is silk protein and a graphene film, can react to humidity changes and temperature changes in the environment, can also react to stretching, can generate corresponding changes through changes of different environmental factors, realizes sensing of the external environment, and is simple in manufacturing method, small in device size, flexible and wearable, and wide in application prospect.