Naturally occurring fossil fuels are the major resource of energy in our everyday life, but with the huge technological development over the years and subsequent energy demand, the reserve of this energy resource is depleting at an alarming rate, which will challenge our net energy resources in the near future. Thus, an alternative sustainable energy resource involving biomass and bio-refinery has become the most emerging and demanding approach, where biofuels can be derived effectively from abundant biomass via valuable chemical intermediates like 5-hydroxymethylfurfural (5-HMF). 5-HMF is a valuable platform chemical for the synthesis of fuel and fine chemicals. Herein, we report the synthesis of the organically functionalized porous aluminum phosphonate materials: Ph-ALPO-1 in the absence of any template and Ph-ALPO-2 by using 1,3-diaminopropane-N,N,N′,N′-tetraacetic acid as a small organic molecule template and phenylphosphonic acid as a phosphate source. These hybrid phosphonates are used as acid catalysts for the synthesis of 5-HMF from carbohydrates derived from biomass resources. These Ph-ALPO-1 and Ph-ALPO-2 materials catalyzed the dehydration of fructose to 5-HMF with total yields of 74.6% and 90.7%, respectively, in the presence of microwave-assisted optimized reaction conditions.