The invention discloses a groove gate high voltage device based on a super junction drain field plate and a manufacturing method of the groove gate high voltage device. The groove gate high voltage device sequentially comprises a lining, a GaN buffer layer, a GaN channel layer, an AlN isolation layer, an intrinsic AlGaN layer and an AlGaN barrier layer. A source electrode, a grid electrode and a composite drain electrode are arranged on the AlGaN barrier layer at intervals. Linear AlGaN layers are further arranged between the grid electrode and the composite drain electrode and between the source electrode and the grid electrode. A p-GaN layer is arranged on the linear AlGaN layer between the grid electrode and the composite drain electrode. A base electrode is arranged on the p-GaN layer. A gate source field plate is further formed on the portion, located above the linear AlGaN layer, of the grid electrode in the direction towards the source electrode. Passivation layers are further deposited on the top layer of the structure at intervals. Thickened electrodes are deposited in intervals of the passivation layers. Both the aim of improving the device breakdown voltage and the aim of reducing on resistance are taken into consideration; meanwhile, the groove gate structure is adopted, the regulation and control effect of the grid electrode on the channel 2 DEG is enhanced, and the frequency performance of the device is improved.