Root-deck cracks, a prominent form of subsurface damage observed in orthotropic steel decks (OSDs), pose significant challenges to maintaining structural integrity. Early detection of these cracks is crucial to prevent further deterioration. This paper introduces novel and robust techniques for processing response signals obtained from the Pulsed Eddy Current Technique (PECT) using phase space analysis. The proposed methods aim to improve sensitivity and noise handling capabilities by employing an appropriate damage index derived from comprehensive phase space analysis, enabling effective detection of subsurface cracks in OSDs. A numerical study demonstrates the effectiveness of the proposed methods in detecting crack length change as small as 1 mm from the bottom of a 12 mm steel plate, with the Change in Phase Space Topology (CPST) identified as a suitable damage index. Furthermore, the newly proposed signal processing techniques allow for a more comprehensive interpretation of response signals for subsurface damage detection, encapsulating the extent of damage within a single value, even in the presence of small crack lengths near the bottom of the steel plate and noise. As a result, the proposed methods overcome the limitations of conventional approaches and offer promising prospects for enhanced subsurface crack detection in OSDs.