Chemical engineering optimization from a batch process to continuous flow in liquid-phase hydrogenation brings a significant improvement in efficiency. However, its further application is limited due to the severe pressure drop and tube blockage problems in a powder-form catalyst fixed-bed reactor, especially for nanocarbon-supported catalysts. In this work, spherical monoliths containing oxygenated carbon nanotube (oCNT)-supported Pd nanoparticles (ca. average size of 2 mm) are fabricated via an in situ gelation method and applied for cinnamaldehyde (CAL) selective hydrogenation in a continuous-flow system. The simulated results by the computational fluid dynamics–discrete element method (CFD–DEM) coupled method show that the pressure drop of the monolith catalyst bed is maintained within 0.4 Pa. The Pd/oCNT monolithic catalyst exhibits excellent CAL conversion of 85.8% and hydrocinnamaldehyde (HCAL) selectivity of 93.5% within a high weight hourly space velocity (WHSV) of 0.012 s–1 at mild reaction conditions (30 °C, 3 bar). The catalyst maintains robust catalytic activity and HCAL selectivity (>93%) under varied reaction temperatures (30/60 °C), H2 partial pressures (3–10 bar), and WHSVs (0.012–0.184 s–1) and a stable reaction activity for more than 60 h time on stream, revealing the possibility in industrial hydrogenation reactions. The catalytic activity of the monolithic catalyst is determined by the surface properties of the carbon nanotubes and the chemical interactions between Pd nanoparticles and supports. The oxygenated functional groups and surface defects on oCNTs are beneficial for strong chemical interaction with Pd species, which forms abundant electron-deficient Pdδ+ species to facilitate C═C hydrogenation. This study puts forward insights into and perspectives for selective hydrogenation reactions in both electronic structure tuning of the active phase at the atomic scale and fabrication of monolithic catalysts at the macroscopic scale.