With the proliferation of Location-based Social Networks (LBSNs), user check-in data at Points-of-Interest (POIs) has surged, offering rich insights into user preferences. However, sequential POI recommendation systems always face two pivotal challenges. A challenge lies in the difficulty of modeling time in a discrete space, which fails to accurately capture the dynamic nature of user preferences. Another challenge is the inherent sparsity and noise in continuous POI recommendation, which hinder the recommendation process. To address these challenges, we propose counterfactual user sequence synthesis with continuous time dynamic preference modeling (CussCtpm). CussCtpm innovatively combines Gated Recurrent Unit (GRU) with neural Ordinary Differential Equations (ODEs) to model user preferences in a continuous time framework. CussCtpm captures user preferences at both the POI-level and interest-level, identifying deterministic and non-deterministic preference concepts. Particularly at the interest-level, we employ GRU and neural ODEs to model users' dynamic preferences in continuous space, aiming to capture finer-grained shifts in user preferences over time. Furthermore, CussCtpm utilizes counterfactual data augmentation to generate counterfactual positive and negative user sequences. Our extensive experiments on two widely-used public datasets demonstrate that CussCtpm outperforms several advanced baseline models.