Provided are an intelligent decision-making and control method and system for a microchemical reaction in stepwise sulfidation of a high arsenic-contained waste acid from copper smelter. Microchemical information from the real-time monitoring module is acquired by the intelligent decision-making module. A stage combination for a sulfidation reaction is determined based on a concentration of arsenic in raw waste acid. A total amount of arsenic and an amount of hydrogen sulfide to be added at a first stage are calculated based on a valence state and concentration of arsenic in and a flow rate of inflow at the first stage, and a total amount of arsenic and an amount of hydrogen sulfide to be added at a second stage are calculated based on a valence state and concentration of arsenic in and a flow rate of inflow at the second stage.