Catalytic hydrodechlorination (HDC) has been considered as a promising method for the treatment of wastewater containing chlorinated organic pollutants. A continuous flow Pd/carbon nanotube (CNT)-Ni foam micro reactor system was first developed for the rapid and highly efficient HDC with formic acid (FA) as a hydrogen source. This micro reactor system, exhibiting a higher catalytic activity of HDC than the conventional packed bed reactor, reduced the residence time and formic acid consumption significantly. The desired outcomes (dichlorination >99.9%, 4-chlorophenol outlet concentration <0.1 mg/L) can be obtained under a very low FA/substrate molar ratio (5:1) and short reaction cycle (3 min). Field emission scanning electron microcopy (FESEM) and deactivation experiment results indicated that the accumulation of phenol (the main product during the HDC of chlorophenols) on the Pd catalyst surface can be the main factor for the long-term deactivation of the Pd/CNT-Ni foam micro reactor. The catalytic activity deactivation of the micro reactor could be almost completely regenerated by the efficient removal of the absorbed phenol from the Pd catalyst surface.