Neutralization with liquid digestate and CO2 was compared herein to adjust the pH of lime-treated corn stover. The effects on the thermophilic (55 °C) anaerobic digestion were also analyzed. Liquid digestate neutralization (LDN) caused a decrease in pH from 10.5 to 7.5 in 60 h and accumulation of acetic/isobutyric acids. The CO2 neutralization (CN) under solid-state conditions reduced the pH from 10.5 to 8.5 in 30 min, which is faster than that of LDN and did not affect the subsequent anaerobic digestion. Biomethane production rate indicates that LDN contributed to the performance of anaerobic digestion, but this was not sufficient to compensate for the loss of total biomethane yield, resulting in a negative net profit (i.e., revenue from increased energy production minus reagent cost). For CN under solid-state conditions, the biomethane production was highest in both liquid- and solid-state anaerobic digestion, and also obtained a net profit of 98.74–100.89 RMB/tonne dry biomass. Therefore, the solid-state condition CN is a more efficient and economic method for adjusting initial pH of lime-treated corn stover.