In this paper, we reported an ultrasensitive terahertz (THz) metamaterial biosensor based on a silicon pillar array with precisely designed structures, which presented highly sensitive detection for typical tumor markers. The structure of the silicon pillar array is fabricated on BF33 glass through a bonding and etching process, which exhibits a low loss with a Q factor of 27. It is indicated that this silicon pillar array-based dielectric metamaterial could be used as a biosensor with lower detection limits and higher sensitivity. The biosensor reveals a low detection limit of 1 ng/mL for CA125 and 0.1 ng/mL for HER2 and exhibits a linear response for the logarithm of concentration of the two tumor marks in the range of 1 ng/mL to 10 μg/mL. These results demonstrate that this biosensor is able to offer the capability for highly sensitive tumor marks detection, with noteworthy potential applications in cancer diagnosis.