Gold nanorods have great potential in a variety of applications because of their unique physical properties. In this article, we present the layer-by-layer (LbL) assembly of thin films containing positively charged gold nanorods that are covalently functionalized by cationic thiol molecules. The cationic gold nanorods are uniformly distributed in ultrathin nanocomposite LbL thin films. We studied the collective surface plasmon resonance coupling in the LbL films via UV-visible spectroscopy and evaluated their application in the surface-enhanced Raman scattering detection of rhodarnine 6G probe molecules. Furthermore, we successfully manufactured freestanding nanoscale thin films containing multilayers of gold nanorods with a total thickness of less than 50 nrn. The surface morphology and their optical and mechanical properties were systematically investigated, and the polycationic gold nanorods were found to play an important role in manipulating the properties of the nanocomposite thin films. Our findings reveal that such nanorods are excellent building blocks for constructing functional LbL films with tunable plasmonic behavior and robust mechanical properties.