Articulated objects, such as laptops and drawers, exhibit significant challenges for 3D reconstruction and pose estimation due to their multi-part geometries and variable joint configurations, which introduce structural diversity across different states. To address these challenges, we propose KineDiff3D: Kinematic-Aware Diffusion for Category-Level Articulated Object Shape Reconstruction and Generation, a unified framework for reconstructing diverse articulated instances and pose estimation from single view input. Specifically, we first encode complete geometry (SDFs), joint angles, and part segmentation into a structured latent space via a novel Kinematic-Aware VAE (KA-VAE). In addition, we employ two conditional diffusion models: one for regressing global pose (SE(3)) and joint parameters, and another for generating the kinematic-aware latent code from partial observations. Finally, we produce an iterative optimization module that bidirectionally refines reconstruction accuracy and kinematic parameters via Chamfer-distance minimization while preserving articulation constraints. Experimental results on synthetic, semi-synthetic, and real-world datasets demonstrate the effectiveness of our approach in accurately reconstructing articulated objects and estimating their kinematic properties.