The Gaoligong shear zone (GLGSZ) and Lancangjiang shear zone (LCJSZ) are two major large-scale shear zones southeast of Eastern Himalayan Syntaxis (EHS) and play important roles in the accommodation of the intracontinental deformation in Southeast Asia. The two shear zones, which are mainly composed of high-grade metamorphic rocks and have long been regarded as the Precambrian basement of this area, are gradually merged northward and become tectonically amalgamated from Fugong to Gongshan area. Structural and kinematic analyses reveal that the amalgamation area has experienced strongly partitioned dextral transpression. N–S trending tight to isoclinal folds, sub-vertical foliation and sub-horizontal lineation are ubiquitously developed both within the shear zones and the Carboniferous flysch sediments of Baoshan block in between. Micro- and macro-kinematic indicators such as CS structures, rotated porphyroclasts, asymmetric shear folds, sheath folds, domino and boudin structures suggest that the shear sense of the GLGSZ and LCJSZ is dextral in the amalgamation area. Comparative analyses of strata reveal that the Baoshan block is aligned with south Qiangtang block and the Lanping–Simao block was aligned with north Qiangtang block prior to the Cenozoic large scale tectonic extrusion and rotation. The amalgamation area, which has progressively switched positions from northeast of EHS to east and southeast of EHS, is just located at the neck of the large scale boudin of south Qiangtang–Baoshan block. A boudin model is proposed for the tectonic amalgamation of the GLGSZ and LCJSZ from Fugong to Gongshan area in response to the continued northward convergence between Indian plate and Eurasian plate since early Eocene, resistance of South China block, southeastward extrusion and clockwise rotation of Baoshan block around EHS.