Hierarchically ordered mesocellular mesoporous silica materials (HMMS) were synthesized using a single structure-directing agent. The mesocellular pores are synthesized without adding any pore expander; the pore walls are composed of SBA-15 type mesopores. Small-angle X-ray scattering revealed the presence of uniform pore structures with two different sizes. Using HMMS as a nanoscopic template, hierarchically ordered mesocellular mesoporous carbon (HMMC) and polymer (HMMP) materials were synthesized. HMMS was used as a host for enzyme immobilization. To improve the retention of enzymes in HMMS, we adsorbed enzymes, and then employed crosslinking using glutaraldehyde (GA). The resulting crosslinked enzyme aggregates (CLEAs) show an impressive stability with extremely high enzyme loadings. For example, 0.5 g α-chymotrypsin (CT) could be loaded in 1 g of silica with no activity decrease observed with rigorous shaking over one month. In contrast, adsorbed CT without GA treatment resulted in a lower loading, which further decreased due to continuous leaching of adsorbed CT under shaking. The activity of crosslinked CT aggregates in HMMS was ≈10 times higher than that of the adsorbed CT, which represents a 74-fold increase in activity per unit weight of HMMS due to higher CT loading.