The main purpose of the present study was to investigate the effect of motivation on emotional stimulus processing under the different cognitive load by combining the emotional flanker task with the number task. The present study used pictures with different emotional dimensions of valence as the target stimuli and pictures with different emotional dimensions of motivation as the interference stimuli. The present study included two experiments both using a 2 (cognitive load: high vs. low) × 2 (the motivation of interference stimuli: high vs. low) × 2 (the valence of target stimulus: positive vs. negative) mixed design. The procedure of the two experiments was the same ones. At the beginning of each experiment, a random number presented at the center of the screen (two digits under the low cognitive load, three digits under the high cognitive load). Participants were asked to remember this number, and keep counting from this number and reporting loudly (take the number to plus 2 under the low cognitive load condition, reduce 6 under the high cognitive load condition) in the following flanker task. In the flanker task, participants’ main task was to ignore the pictures presented on the one side of the screen and evaluate the valence of well-defined emotional stimuli (words in the Experiment1 and pictures in the Experiment2) as quickly as possible by pressing the “J” key for positive stimuli and the “F” key for negative stimuli. The Experiment 1 used positive/ negative words as target stimuli and pictures with high/low motivation as the interference stimuli. Results showed that there was a significant interaction among the cognitive load, the valence of target stimulus and the motivation of interference stimuli. Under the high cognitive load condition, the response times (RTs) were shorter for positive words relative to negative words in the high motivation condition, while the RTs were shorter for negative words relative to positive words in the low motivation condition. However, no significant difference was found under the low cognitive load condition. That was to say, only in the high cognitive load condition, high motivation facilitated positive emotional processing and low motivation facilitated negative emotional processing, indicating that motivation had an influence on the processing of emotional stimuli in the high cognitive load condition. What’s more, the RTs under the high cognitive load condition were shorter than those under the low cognitive load condition besides the RTs for positive words in high motivation condition. In the Experiment 2, positive/negative pictures were used as target stimuli and pictures with high/low motivation were used as the interference stimuli. The results of Experiment 2 were almost the same as the results of the Experiment 1. That was, under the high cognitive load condition, high motivation facilitated the processing of positive emotional stimuli, while low motivation facilitated the processing of negative emotional stimuli, and no difference was found under the low cognitive load condition. What’s more, the RTs under the high cognitive load condition were shorter than those under the low cognitive load condition besides the RTs for positive words in high motivation condition and the RTs for negative words in low motivation condition. In summary, under the high cognitive load condition, high motivation facilitated positive emotional processing, while low motivation facilitated negative emotional processing. Moreover, high cognitive load hindered the emotional processing.