Flow structures, hemodynamics and the hydrodynamic surgical pathway resistances of the final stage functional single ventricle reconstruction, namely the total cavopulmonary connection (TCPC) anatomy, have been investigated extensively. However, the second stage surgical anatomy (i.e., bi-directional Glenn or hemi-Fontan template) has received little attention. We thus initiated a multi-faceted study, involving magnetic resonance imaging (MRI), phase contrast MRI, computational and experimental fluid dynamics methodologies, focused on the second stage of the procedure. Twenty three-dimensional computer and rapid prototype models of 2nd stage TCPC anatomies were created, including idealized parametric geometries (n = 6), patient-specific anatomies (n = 7), and their virtual surgery variant (n = 7). Results in patient-specific and idealized models showed that the Glenn connection template is hemodynamically more efficient with (83% p = 0.08 in patient-specific models and 66% in idealized models) lower power losses compared to hemi-Fontan template, respectively, due to its direct end-to-side anastomosis. Among the several secondary surgical geometrical features, stenosis at the SVC anastomosis or in pulmonary branches was found to be the most critical parameter in increasing the power loss. The pouch size and flare shape were found to be less significant. Compared to the third stage surgery the hydrodynamic resistance of the 2nd stage is considerably lower (both in idealized models and in anatomical models at MRI resting conditions) for both hemi- and Glenn templates. These results can impact the surgical design and planning of the staged TCPC reconstruction.