The sporopollenin precursor from tapetum deposits inside a tetrad to form the outer pollen wall with ornate geometric pattern. In the knockout mutant of a DNA methyltransferase EFD (Exine Formation Defect), pollen wall pattern is defective which leads to pollen rupture and male sterility. In this study, we found efd was also defective in sporopollenin synthesis. The overexpression of HB21, a member of homeodomain family, is responsible for the defective of both sporopollenin synthesis and pollen wall pattern formation in efd. The methylation of four cytosines in the 1458~1478 genomic sequence of HB21 was reduced in efd. That the replacement of C1467A and C1476A restored the expression of HB21 suggest that EFD represses HB21 expression through DNA methylation. We further demonstrated that HB21 directly repressed the expression of genes involved in sporopollenin precursor synthesis (CYP703A2) and pollen wall pattern determination (Cals5 and RPG1/SWEET8). This indicates that HB21 is a negative regulator to coordinate the pollen wall material synthesis in tapetum and pollen wall pattern determination inside tetrad for outer pollen wall formation. This process is further regulated by methylation of EFD.