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Determining the similarity between dynamical systems remains a long-standing challenge in both machine learning and neuroscience. Recent works based on Koopman operator theory have proven effective in analyzing dynamical similarity by examining discrepancies in the Koopman spectrum. Nevertheless, existing similarity metrics can be severely constrained when systems exhibit complex nonlinear behaviors across multiple temporal scales. In this work, we propose **KoopSTD**, a dynamical similarity measurement framework that precisely characterizes the underlying dynamics by approximating the Koopman spectrum with explicit timescale decoupling and spectral residual control. We show that KoopSTD maintains invariance under several common representation-space transformations, which ensures robust measurements across different coordinate systems. Our extensive experiments on physical and neural systems validate the effectiveness, scalability, and robustness of KoopSTD compared to existing similarity metrics. We also apply KoopSTD to explore two open-ended research questions in neuroscience and large language models, highlighting its potential to facilitate future scientific and engineering discoveries. Code is available at [link](https://github.com/ZhangShimin1/KoopSTD).