We propose a new integrated target tracking, recognition and segmentation algorithm, called ATR-Seg, for infrared imagery. ATR-Seg is formulated in a probabilistic shape-aware level set framework that incorporates a joint view-identity manifold (JVIM) for target shape modeling. As a shape generative model, JVIM features a unified manifold structure in the latent space that is embedded with one view-independent identity manifold and infinite identity-dependent view manifolds. In the ATR-Seg algorithm, the ATR problem formulated as a sequential level-set optimization process over the latent space of JVIM, so that tracking and recognition can be jointly optimized via implicit shape matching where target segmentation is achieved as a by-product without any pre-processing or feature extraction. Experimental results on the recently released SENSIAC ATR database demonstrate the advantages and effectiveness of ATR-Seg over two recent ATR algorithms that involve explicit shape matching.