Apolipoprotein B100 (apoB) is the major protein of the cholesterol-rich low-density lipoprotein (LDL). Calculating or measuring LDL or VLDL cholesterol may not reflect the actual number of these atherogenic particles and apoB does reflect a better assessment of total athrogenic burden to the vascular system which make measuring apoB particularly important. In this work, a simple and sensitive method has been developed to determine picoliter apoB-100s using the PMMA microfluidic chip coupled with three-electrode electrochemical detection system. After the PMMA microchannel being modified with poly(ethleneimine) (PEI) which contains abundant NH2 groups, the apoB-100 antibodies can be easily absorbed on the surface of the microchannel. Afterwards, alkaline phosphatase (ALP) can be labeled in the microchannel by ELISA method. The inner surface of the PMMA microchannel has been assembled with poly(ethyleneimine) (PEI) which can immobilize apoB-100. The PEI modification has been characterized by ATR-FTIR. The substrate containing 30 μg mL-1 4-aminophenylphophate momosodium salt (p-APP) can be catalyzed by ALP when it flows in the microchannel to produce PAP at the outlet whose electrical signal can be recorded by the three-electrode detection system. This method performs very well and gives a detect limitation of 1 pg mL-1. We achieved a detectable linear concentration range of 1-800 pg mL-1 by different pulse voltammetry (DPV). A real serum sample was also detected by this microchip-based immunoassay method. The result shows that this kind of method is practicable and has the potential application in clinical analysis and diagnosis.