Sensitivity and credibility detecting histamine (HA) as an important neurotransmitter in biofluids is of importance in analytical science and physiology. Surface-enhanced Raman spectroscopy (SERS) is able to realize the high sensitivity with single molecules level, but providing the high sensitivity for HA with a small cross section remains a challenge. Here we develop the metal complex-based SERS nanoprobe nitrilotriacetic acid-Ni2+ (NTA-Ni2+) combined with self-assemble Au NPs active substrates for sensitive detection of HA. The NTA-Ni2+ can capture the HA molecules close to Au NPs substrates and then amplify the Raman signals of HA owing to the formation of a complex of NTA-Ni2+-HA. The self-assemble Au film through the evaporation-driven method can provide the high-density hot spots substrate with high stability and reproducibility. The NTA-Ni2+ decorated Au NPs as nanoprobe responds to HA with 1 μM level of sensitivity. More importantly, the developed SERS nanoprobe composing of NTA-Ni2+ and self-assemble Au NPs can be utilized to detect and monitor the HA spiked into serum, indicating the potential prospect in analysis of HA in complex specimen.