The emotion-cognition interaction has been extensively explored by using threat-related stimuli, such as fearful and angry faces, as well as threatening animals. It has been suggested that threat signals conveyed by the complex threatening stimuli are partially attributed to their geometric structures, such as sharp elements in contour. The present study was aimed to investigate whether such geometric shapes had similar influence as threatening stimuli on visual size perception by using downward-pointing V shapes as primes and measuring the modulation effect on the classic Ebbinghaus illusion. The results showed that relative to curved-shape primes, V-shape primes significantly reduced the illusion strength when the primes were presented with relatively long duration (150 ms) regardless of their eccentricity (4° or 8° from screen center). However, when the primes were displayed with short duration (16.7 ms), significant threat-related modulation effect was only observed with central instead of peripheral presentation. Moreover, the modulation effect vanished with excitation of right dorsolateral prefrontal cortex via intermittent theta burst stimulation. The findings provide clear evidence that threat-related geometric shapes can affect visual perception in a similar way as threatening stimuli, which requires detail processing of the geometric shapes and relies on top-down cognitive control from prefrontal cortex.