Palmatine is a protoberberine alkaloid separated from several plants and application as an anti-inflammatory and antibacterial agent in the therapy of gastrointestinal and genitourinary disorder. Thus, the fast quantification of palmatine is important in clinic medical assays. Herein, we report simple, fast and sensitive colorimetric visualization and surface-enhanced Raman spectroscopy (SERS) dual-mode detection of palmatine basing on bimetallic size tunable silver shell capped gold nanoparticles (Au@Ag NPs). Interesting, the best signals output for dual-mode sensing of palmatine were both 5 nm Ag shell thickness of Au@Ag NPs. Meanwhile, we found that the addition of NaHSO4 significantly improves the aggregating sensitivity of Au@Ag NPs to trace palmatine. Upon exposure to 0.1 μM level palmatine, NaHSO4-optimized Au@Ag NPs solution exhibits a highly sensitive color change from orange to green and rapid aggregation kinetics within the initial 5 min, which can directly be seen with the naked eye and monitored by UV-vis absorbance spectra. In addition, we measured palmatine by SERS with the excellent enhancement effect of Au@Ag NPs for further increase the sensitivity and selectivity. More importantly, other protoberberine alkaloids do not interfere with this dual-mode sensor due to the different interaction force between Au@Ag NPs and these alkaloids, and the applicability of the sensor is well demonstrated in real samples with satisfactory results. This provide a fast and simple assay for the rapid detection of palmatine in traditional Chinese medicine, the limit of detection (LOD) is 0.13 μM by the naked eye and 0.10 μM by UV-vis spectroscopy. Therefore, the size-tunable of NaHSO4-optimized Au@Ag NPs can be used not only as a naked-eye sensor of palmatine, but also as a highly selective SERS probe.