Heavy metal pollution is causing a great threat to ecological environment and public health, which needs an efficient strategy for monitoring. A portable microfluidic electrochemical sensing system was developed for the determination of heavy metal ions. Herein, the detection of Pb2+ was chosen as a model, and a microfluidic electrochemical sensing chip relying on a smartphone-based electrochemical workstation was proposed for rapid detection Pb2+ with the assistance of thermocapillary convection result from the formed temperature gradient. The 3D Ag-rGO-f-Ni(OH)2/NF composites, prepared by one-step hydrothermal method without any Ni precursor salt, were used to further amplify electrochemical signals under the synergistic effect of thermocapillary convection. The thermocapillary convection could accelerate the preconcentration process and shorten the detection time (save 300 s of preconcentration time). The fabricated system exhibited the exceptional competence for monitoring of Pb2+ range from 0.01 μg/L to 2100 μg/L with a low detection limit (LOD) of 0.00464 μg/L. Furthermore, this portable system has been successfully demonstrated for detecting Pb2+ (0.01 μg/L to 2100 μg/L) in river water (LOD = 0.00498 μg/L), fish (LOD = 0.00566 μg/L) and human serum samples (LOD = 0.00836 μg/L), and the results were consistent with inductively coupled plasma-mass spectrometry (ICP-MS). The proposed novel sensing platform provides a cost-effectiveness, rapidly responding and ease-to-use pathway for analysis of heavy metal ions in real samples and shows great potential in point-of-care testing.