The invention discloses an automatic control system for a papermaking pulping section. The system comprises a host computer, an emergency stop module, a control module, a sensor module and a controlled device; the host computer, the emergency stop module and the control module are electrically controlled with the controlled device respectively; the host computer is used for displaying the runningstates=, configuration control parameters and the display process step of every device; the emergency stop module is used for urgently stopping the controlled device to ensure the safety of personneland equipment; and the control module is used for executing control logics, receiving the state information of the controlled device, collected by the sensor module and sending a control instruction to the controlled device. The invention also provides a running method. The running method is applied to the automatic control system of the papermaking pulping section. The system and the method makethe pulping section realize the unattended fully-automatic running, so the labor cost of enterprises is greatly reduced. Continuous uninterrupted cycle production is also achieved, so the production efficiency is improved.