Motor variability is inevitable in human body movements and has been addressed from various perspectives in motor neuroscience and biomechanics: it may originate from variability in neural activities, or it may reflect a large number of degrees of freedom inherent in our body movements. How to evaluate motor variability is thus a fundamental question. Previous methods have quantified (at least) two striking features of motor variability: smaller variability in the task-relevant dimension than in the task-irrelevant dimension and a low-dimensional structure often referred to as synergy or principal components. However, the previous methods cannot be used to quantify these features simultaneously and are applicable only under certain limited conditions (e.g., one method does not consider how the motion changes over time, and another does not consider how each motion is relevant to performance). Here, we propose a flexible and straightforward machine learning technique for quantifying task-relevant variability, task-irrelevant variability, and the relevance of each principal component to task performance while considering how the motion changes over time and its relevance to task performance in a data-driven manner. Our method reveals the following novel property: in motor adaptation, the modulation of these different aspects of motor variability differs depending on the perturbation schedule.