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Purpose The study aims to display the bubbles' evolution in the shear layer and their relationship with the pressure fluctuations. Furthermore, the coherent structures of the first six modes are extracted, in order to provide insight into their temporal and spatial evolution and determine the relationship between cavitating bubbles and coherent structures. Design/methodology/approach In the present study, numerical simulations of submerged jet cavitating flow were carried out at a cavitation inception condition inside an axisymmetric cavity using the large eddy simulation (LES) turbulence model and the Schnerr-Sauer (S-S) cavitation model. Based on snapshots produced by the numerical simulation, dynamic mode decomposition (DMD) was performed to extract the three-dimensional coherent structures of the first six modes in the shear layer. Findings The cavitating bubbles in the shear layer are deformed to elongated ellipsoid shapes by shear forces. The significant pressure fluctuations are induced by the collapse of the biggest bubble in the group. The first mode illustrates the mean characteristics of the flow field. The flow in the peripheral region of the shear layer is mainly dominated by large-scale coherent structures revealed by the second and third modes, while different small-scale coherent structures are contained in the central region. The cavitating bubbles are associated with small size coherent structures as the sixth or higher modes. Practical implications This work demonstrates the feasibility of LES for high Reynolds number shear layer flow. The dynamic mode decomposition method is a novel method to extract coherent structures and obtain their dynamic information that will help us to optimize and control the flow. Originality/value (1) This paper first displays the three-dimensional coherent structures and their characteristics in the shear layer of confined jet flow. (2) The relationship of bubbles shape and pressure fluctuations is illustrated. (3) The visualization of coherent structures benefits the understanding of the mixing process and cavitation inception in jet shear layers.