We present LTM3D, a Latent Token space Modeling framework for conditional 3D shape generation that integrates the strengths of diffusion and auto-regressive (AR) models. While diffusion-based methods effectively model continuous latent spaces and AR models excel at capturing inter-token dependencies, combining these paradigms for 3D shape generation remains a challenge. To address this, LTM3D features a Conditional Distribution Modeling backbone, leveraging a masked autoencoder and a diffusion model to enhance token dependency learning. Additionally, we introduce Prefix Learning, which aligns condition tokens with shape latent tokens during generation, improving flexibility across modalities. We further propose a Latent Token Reconstruction module with Reconstruction-Guided Sampling to reduce uncertainty and enhance structural fidelity in generated shapes. Our approach operates in token space, enabling support for multiple 3D representations, including signed distance fields, point clouds, meshes, and 3D Gaussian Splatting. Extensive experiments on image- and text-conditioned shape generation tasks demonstrate that LTM3D outperforms existing methods in prompt fidelity and structural accuracy while offering a generalizable framework for multi-modal, multi-representation 3D generation.