Abstract: Conditional score-based diffusion model (SBDM) is for conditional generation of target data with paired data as condition, and has achieved great success in image translation. However, it requires the paired data as condition, and there would be insufficient paired data provided in real-world applications. To tackle the applications with partially paired or even unpaired dataset, we propose a novel Optimal Transport-guided Conditional Score-based diffusion model (OTCS) in this paper. We build the coupling relationship for the unpaired or partially paired dataset based on $L_2$-regularized unsupervised or semi-supervised optimal transport, respectively. Based on the coupling relationship, we develop the objective for training the conditional score-based model for unpaired or partially paired settings, which is based on a reformulation and generalization of the conditional SBDM for paired setting. With the estimated coupling relationship, we effectively train the conditional score-based model by designing a ``resampling-by-compatibility'' strategy to choose the sampled data with high compatibility as guidance. Extensive experiments on unpaired super-resolution and semi-paired image-to-image translation demonstrated the effectiveness of the proposed OTCS model. From the viewpoint of optimal transport, OTCS provides an approach to transport data across distributions, which is a challenge for OT on large-scale datasets. We theoretically prove that OTCS realizes the data transport in OT with a theoretical bound.