This work aims to develop a multihole atmospheric pressure plasma jet (APPJ) device to increase the plasma area and apply it to a continuous seed treatment system. Broccoli seed was used to study the effects of an atmospheric pressure plasma jet on seed germination and growth rate. An argon flow rate of 4.2 lpm, a plasma power of 412 W, and discharge frequency of 76 kHz were used for seed treatment. The contact angle decreased strongly with the increase in treatment time from 20 s to 80 s. The broccoli seed’s outer surface morphology seemed to have been slightly modified to a smoother surface by the plasma treatment during the treatment time of 80 s. However, the cross-sectional images resulted from Synchrotron radiation X-ray tomographic microscopy (SRXTM) confirmed no significant difference between seeds untreated and treated by plasma for 80 s. This result indicates that plasma does not affect the bulk characteristics of the seed but does provide delicate changes to the top thin layer on the seed surface. After seven days of cultivation, the seed treated by plasma for 30 s achieved the highest germination and yield.