Data augmentation is an effective technique for regularizing deep networks, which helps to enhance the generalizability and robustness of the model. However, in the field of medical imaging, traditional data augmentation techniques such as cropping, rotation, and degradation may inadvertently alter the critical characteristics of pathological lesions. Conventional semantic augmentation methods, such as altering the color and contrast of the object background, may also affect the structural features of medical images in uncontrolled semantic directions. Such operational conditions compromise the model's diagnostic reliability in medical contexts. To address this issue, we propose a surprisingly efficient implicit augmentation-invariant learning strategy (AILS) via variational Bayesian inference on differentially constrained feature manifolds. Parameterizing probability measures over tangent space through deep networks enables precise estimation of semantic direction distributions. Subsequently, geodesic-aware semantic features are sampled from the reparameterized variational posterior, achieving semantic-consistent augmentation. Simultaneously, to mine augmentation distribution invariance, we design the AiHLoss, which constrains the augmentation distribution to facilitate the network to learn augmentation invariance. Extensive experiments demonstrate that AILS exhibits high performance on public medical image datasets, outperforming existing augmentation methods.