We present the latest and the near-future design of the KOTO data-acquisition system. The KOTO experiment is searching for the rare kaon decay $K_L^0\to\pi^0\nu\overline{\nu}$, which is sensitive to New Physics beyond the Standard Model due to the small theoretical uncertainty. In order to efficiently collect the candidate events under the high-intensity $K_L^0$ beam, the two-level trigger system was hence developed. The pulses from nearly 4000 channels were continuously digitized and pipelined with the depth of 5.2 $\mu s$ at customized flush analog-to-digital converters (FADC) for trigger-processing. The level-1 trigger required the total energy in the calorimeter and the absence of hits in the veto counters. The level-2 trigger required two electromagnetic showers (clusters) in the calorimeter. The system dead time was measured to be 0.16 $\mu s$ and the live time ratio was 99%. In the near future, the customized module with multiple optical connectors will be used to collect all data from the FADCs and perform the event-building. The complete events are sent to the PC farms via 10 Gbps throughput for more sophisticated trigger decisions. This not only improves the data collection efficiency but broadens the coverage of physics topics for the KOTO experiment.