The invention provides an intelligent analysis system and method for magnetic flux leakage detection data in a pipeline. The process comprises the following steps: adopting time domain-based sparse sampling and KNN-softmax data complete set construction module, obtaining a complete magnetic flux leakage data set; a pipeline connection assembly discovery method based on combination of selective search and a convolutional neural network is adopted in the discovery module to obtain the accurate position of the weld joint; adopting an abnormal candidate region searching and identifying method based on a Lagrangian multiplication frame and multi-source magnetic flux leakage data fusion in the discovery model to find out defective magnetic flux leakage signals; Adopting a defect quantification method based on a random forest in a quantification module to obtain a defect size; a pipeline solution improved based on the ASME B31G standard is adopted in the solution module, and an evaluation result is output. An analysis method is provided from the overall perspective, and pretreatment, connection assembly detection and abnormity detection, defect size inversion and final maintenance decision are achieved.