In clinical practice, single-radiotracer positron emission tomography (PET) is commonly used for imaging. Although multi-tracer PET imaging can provide supplementary information of radiotracers that are sensitive to physiological function changes, enabling a more comprehensive characterization of physiological and pathological states, the gamma-photon pairs generated by positron annihilation reactions of different tracers in PET imaging have the same energy, making it difficult to distinguish the tracer signals. In this study, a multi-latent space guided texture conditional diffusion transformer model (MS-CDT) is proposed for PET tracer separation. To the best of our knowledge, this is the first attempt to use texture condition and multi-latent space for tracer separation in PET imaging. The proposed model integrates diffusion and transformer architectures into a unified optimization framework, with the novel addition of texture masks as conditional inputs to enhance image details. By leveraging multi-latent space prior derived from different tracers, the model captures multi-level feature representations, aiming to balance computational efficiency and detail preservation. The texture masks, serving as conditional guidance, help the model focus on salient structural patterns, thereby improving the extraction and utilization of fine-grained image textures. When combined with the diffusion transformer backbone, this conditioning mechanism contributes to more accurate and robust tracer separation. To evaluate its effectiveness, the proposed MS-CDT is compared with several advanced methods on two types of 3D PET datasets: brain and chest scans. Experimental results indicate that MS-CDT achieved competitive performance in terms of image quality and preservation of clinically relevant information. Code is available at: https://github.com/yqx7150/MS-CDT.