The 100-MeV proton linear accelerator of the Proton Engineering Frontier Project (PEFP) has been developed, and the low-level radio frequency (LLRF) control system for the PEFP 100-MeV accelerator has also been developed. A field stability within +/- 1 degrees in the RF phase and +/- 1% in the RF amplitude is required in the LLRF control system. The prototype LLRF control system was developed and had been operated for the 20-MeV accelerator, but it was necessary to improve the LLRF control system for 100-MeV accelerator operation. For field stability and stable pulse operation of the 1.5-ms pulse width and a 60-Hz repetition rate (duty of 9%), the control scheme of the direct intermediate frequency (IF) signal output from a field programmable gate array (FPGA) board was adopted, and the commercial FPGA board and the LLRF analog system were changed. The IF and the local oscillator (LO) frequency for the feedback control were chosen as 50-MHz and 300-MHz respectively, and the sampling rate for the in-phase, quadrature (IQ) detection was kept at 40-MHz. In the test with a dummy cavity, the RF amplitude and phase were maintained within +/- 0.1% and +/- 0.1 degrees, respectively, for a pulse width of 1.5-ms and a repetition rate of 60-Hz. In the 20-MeV accelerator operation, a field stability within +/- 0.6% in the RF amplitude and +/- 0.3 degrees in the RF phase was measured.