Nanoporous materials have attracted considerable technological interest due to their wide range of applications. In this study, highly ordered nanoporous anodic alumina substrates (NAAS) were fabricated by two-steps anodisation. Radio-frequency (RF) magnetron sputtering was used to deposit ultrathin Cu layers of different morphologies on the top surface of NAAS. From the field emission-scanning electron microscope images, the Cu/NAAS morphologies were tuned from nanoporous ultra-thin Cu layer, to nanoporous-grains of Cu aggregates, then to a continues layer of Cu nanostones as the deposition time increased from 1 to 4 min. The reflection spectra of the Cu/NAAS samples were dominated with localised surface plasmon modes; longitudinal, transverse and higher-order modes. The surface plasmon resonances of the fundamental and higher-order longitudinal modes were shifted to longer wavelengths as the deposition time increased. In addition, the transverse surface plasmon resonances were shifted to longer wavelengths for deposition time ≤3 min (nanoporous Cu film) and suddenly shifted to shorter wavelengths for deposition time ≥4 min (continuous film). The correlations between the structural parameters and the shift of surface plasmon resonance modes were discussed. The strong red-shifted of the surface plasmon modes to the NIR region suggests a unique opportunity for the design of biomedical sensor based on the proposed structures.