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Highlights A novel method is developed for precise control over the structure of 3D anodic aluminum oxide templates, enabling fine-tuning of both the vertical pore diameter and interspace within the templates. 3D carbon tube nanoarrays featuring significantly thinner and denser tubes are constructed as high-quality electrodes for miniaturized filter capacitors. The 3D compactly arranged carbon tube-based capacitor achieves a remarkable specific areal capacitance of 3.23 mF cm−2 with a phase angle of − 80.2° at 120 Hz.