Lateral flow assay (LFA) systems use metal nanoparticles for rapid and convenient target detection and are extensively studied for the diagnostics of various diseases. Gold nanoparticles (AuNPs) are often used as probes in LFAs, displaying a single red color. However, there is a high demand for colorimetric LFAs to detect multiple biomarkers, requiring the use of multicolored NPs. Here, we present a highly sensitive multiplexed colorimetric lateral flow immunoassay by multicolored Plasmon-controlled metal-silica Isoform Nanocomposites (PINs). We utilized the localized surface plasmon resonance effect to create multi-colored PINs by precisely adjusting the distance between the NPs on the surface of PINs through the controlled addition of reduced gold and silver precursors. Through simulations, we also confirmed that the distance between nanoparticles on the surface of PINs significantly affects the color and colorimetric signal intensity of the PINs. We achieved multicolored PINs that exhibit stronger colorimetric signals, offering a new solution for LFA detection with high sensitivity and a 33 times reduced limit of detection (LOD) while maintaining consistent size deviations within 5%. We expect that our PINs-based colorimetric LFA will facilitate the sensitive and simultaneous detection of multiple biomarkers in point-of-care testing.