Multi-joint link is a class of typical structure in aircraft assembly. And the quantification of assembly error is very important to tolerance allocation and assembly quality prediction. A novel error analysis model of multi-joint assembly is established based on linkage mechanism theory. First, a virtual linkage mechanism will be created according to specific structural character and tolerance of joint linkage. And then, the input-output equation of linkage mechanism can be derived by vector method. Subsequently, the coaxiality and coplanarity error analysis models are developed respectively for three-joint and four-joint assembly. Finally, a case study on the elevator & horizontal empennage docking demonstrates the proposed method.