We are upgrading the KOTO data-acquisition system to collect $K_L^0 \to \pi^0 \nu \overline{\nu}$ data efficiently toward a higher $K_L^0$ beam intensity. The upgrade includes the expansion of the data throughput and the third-level trigger decision at the PC farm. The University of Chicago designed electronic modules with numerous high-speed optical links to transfer data from analog-to-digital converters, perform the event-building, and deliver complete events to the PC farm for the level-3 trigger evaluation. By maintaining the loss due to the network congestion to be less than 1%, the maximum event rate was improved from 8k events/sec to 15k events/sec. This limit can be further extended by horizontally connecting more modules if needed.