Silk fibroin (SF) with good biocompatibility can enable an efficient and safe implementation of neural interfaces. However, it has been difficult to achieve a robust integration of patterned conducting materials (multichannel electrodes) on flexible SF film substrates due to the absence of some enduring interactions. In this study, a thermo‐assisted pattern‐transfer technique is demonstrated that can facilely transfer a layer of pre‐set poly(3,4‐ethylenedioxythiophene) (PEDOT) onto the flexible SF substrate through an interpenetrating network of 2 polymer chains, achieving a desired substrate/conductor intertwined interface with good flexibility (≈33 MPa), conductivity (386 S cm−1) and stability in liquid state over 4 months simultaneously. Importantly, this technique can be combined with ink‐jet printing to prepare a multichannel SF‐based neural interface for the electrocorticogram (ECoG) recording and inflammation remission in rat models. The SF‐based neural interface with satisfied tissue conformability, biocompatibility, and bioelectric conductivity is a promising ECoG acquisition tool, where the demonstrated approach can also be useful to develop other SF‐based flexible bioelectronics.