A smartphone-integrated multi-model thermal immunochromatographic assay has been constructed for the detection of histamine by using anti-histamine antibody coupled Cu2−xSe nanoparticles (Cu2−xSe@antibody) as photothermal nanoprobes. Base on a competitive format, the coated histamine antigen on T-line and histamine simultaneously competed for binding the lateral flow photothermal signal probes. With the increase of histamine concentration, the temperature of Cu2−xSe@antibody on T-line was decreased under the 808 nm laser irradiation, which can be monitored via the smartphone-thermal imager combination device. In addition, the color on T-line from nanoprobes gradually disappeared, and the inhibition rate calculated from the obtained temperature on T-line was increased. The smartphone-integrated multi-model thermal immunochromatographic assay enables detection of histamine in the range of 0.1–10.0 μg/L with limit of detection as low as 0.09 μg/L. The histamine concentrations in crab, tuna, saury, mackerel, shrimp were 5.67 mg/kg, 83.73 mg/kg, 14.03 mg/kg, 21.30 mg/kg, 3.22 mg/kg detected by the developed thermal immunochromatographic assay, respectively. The developed multi-model strategy provided good sensitivity, simple operation, effectiveness and practicability for histamine in real samples compared to ultra-performance liquid chromatography-tandem mass spectrometry UPLC-MS/MS and ELISA.