This paper reports a preliminary design of the waveform digitizer “WRX0608A1” for the Jinping Neutrino Experiment (JNE) at the China Jinping Underground Laboratory (CJPL). This digitizer includes a 6-channels compact Peripheral Component Interconnect (cPCI) board with a sampling rate of 1000 MS/s and 13-bit resolution for each channel. It upgrades the original data acquisition system and also is a key part of future 4000-channel readout electronics. Here, we report the system design and performance testing in detail. Key parameters include the effective number of bits (ENOB) being greater than 10 bits, and the quad small form-factor pluggable plus (QSFP+) high-speed signal lane being able to perform long-term error-free transmission under a bandwidth of 10.3125 Gbps. These parameters satisfy the front-end waveform digitization and high-speed data transmission requirements of the current JNE prototype and of future hundred-ton experiments. A joint debugging experiment involving a 30-channel data readout system and a prototype detector is in progress.