Thiram has been widely used in agriculture and may invades the food chain, posing a threat to human health. In this research, a label-free electrochemical cell-based biosensor was presented for in vitro toxicity assessment of thiram. HepG2 cells were cultured on poly-l-lysine@gold nano-flowers functionalized indium tin oxide coated glass electrode (PLL@AuNFs/ITO) to serve as biorecognition elements. AuNFs were electrodeposited on ITO to provide an enlarged specific surface area and benefited the output signal amplification. PLL was selected as an effective biocompatible coating material to facilitate cell adhesion and proliferation, thereby realizing one-step recording of electrochemical signals from thiram-treated cells. With the aid of the differential pulse voltammetry method, the fabricated biosensor was applied to assess the cytotoxicity of thiram. Results showed that the cytotoxicity measured by the fabricated biosensor exhibited a linear relationship related to thiram concentration ranging from 5 to 50 μM with a detection limit of 2.23 μM. The IC50 of thiram obtained by the biosensor was 29.5 μM, which was close to that of conventional MTT assay (30.8 μM). The effects of thiram on HepG2 cells were also investigated via SEM and flow cytometry. Meanwhile, the proposed biosensor was used to evaluate the toxicity of thiram in fruit samples. Results indicated that the toxicity of thiram cannot be ignored even at a low residual concentration in food (≤5 mg/kg). In conclusion, the developed sensor showed excellent sensitivity, stability, and reliability, which provided a great capacity for the convenient toxicity evaluation of thiram residue in food.