The embodiment of the invention provides a workpiece detection and intelligent identification method and system for a complex assembly line. The method includes the steps that when it is detected that workpieces exist at a first station of the complex assembly line, identifiers are set for the detected workpieces, and the identifiers of the coded and detected workpieces are correspondingly stored; and as for first and last conveying points of each section of the complex assembly line, each station, each flow dividing point, each convergence point and each flow dividing and convergence point, when it is detected that the detected workpieces reach the position, the total number of the workpieces corresponding to the position is counted, and workpiece identification codes of the detected workpieces are determined. By means of the scheme, through station counting and logical deduction calculation, the functions of workpiece quantity measurement, workpiece identification, workpiece inspection and maintenance information querying and workpiece automatic flow dividing and convergence are achieved, the automation degree of the complex assembly line can be improved, the labor cost is reduced, and the error rate caused by manual operation is reduced.