The Super-Kamiokande (SK) detector is a ring imaging Cherenkov detector for neutrino physics and proton-decay search and consists of 50000 tons of pure water equipped with about 13000 photo-multipliers (PMTs). The old front-end electronics and online system running for more than one decade were all upgraded in September, 2008 and the data acquisition was started successfully. The new front-end electronics is based on a charge to time converter (QTC) and a multi-hit TDC. TCP/IP based readout channel is implemented to handle large amounts of data. In the new data acquisition (DAQ) scheme, the hardware event-trigger for the data reduction is replaced by processing all the hits in the online farm, so that we are able to lower the threshold of the detection energy for solar neutrino and analyze consecutive events whose time interval is too long to detect in the previous system. To make the new online system to be capable of processing larger dataflow of up to 470MB/s, we utilize Gigabit and 10Gigabit Ethernet techniques and distribute the load over Linux PCs to handle a large amount of data. In this paper, we will describe the design and performance of the new system in the commissioning.