Herein, Janus bimetallic nanorod clusters-poly(aniline) nanocomposites (JRCPCs) with gold nanorod clusters (GNRCs) in side-by-side (SBS) or end-to-end (ETE) configuration are synthesized, and applied to surface-enhanced Raman scattering (SERS)-based biosensing of carcinoembryonic antigen (CEA). Taking advantage of their geometrical and chemical anisotropy, GNRCs in both SBS and ETE configurations are prepared by addition of negatively charged citrate anions and poly(acrylic acid)-block-poly(N-isopropylacrylamide) (PAAc-b-PNIPAM), respectively, to electrostatically interact with cationic cetyltrimethylammonium bromide surfactant on the side of the gold nanorods (GNRs). Subsequently, the JRCPCs are prepared by unidirectional growth of polyaniline and additional growth of Ag onto these GNRCs. JRCPCs with GNRCs in either the SBS or the ETE configuration show strong enhancement of electromagnetic field at both GNR aggregates and GNRC core-Ag shell gaps of bimetallic nanorod cluster components. In particular, because temperature-responsive PAAc-b-PNIPAM of JRCPCs is embedded at GNR junctions, interparticle gaps generated in GNRCs in ETE configuration are controlled via temperature-triggered hydration-dehydration of the PAAc-b-PNIPAM chains such that optical properties are largely changed. With distinct surface functionalities from JRCPCs, SERS-based quantitative analysis of CEA is achieved using JRCPCs as SERS nanoprobes. This work presents the great potential of advanced Janus nanocomposites for SERS-based biosensing applications.