Although many studies have explored the association between negative emotion and working memory, the findings remain controversial. The present study investigated the role of avoidance-motivational intensity in modulating the effect of negative emotion on different processes (maintenance versus manipulation) of verbal and spatial working memory. Two experiments employed the modified delayed match-to-sample paradigms to separate the two processes of verbal and spatial working memory under different emotional states, respectively. In Experiment 1, participants were asked to perform the delayed match-to-sample task with or without reordering the characters (manipulation process of verbal working memory). In Experiment 2, mental rotation was used as the manipulation process of spatial working memory. The results showed that negative emotion only affected the manipulation process, but not the maintenance process. Relative to neutral and low avoidance-motivated negative conditions, the manipulation processes of both types of working memory were impaired under the high avoidance-motivated negative condition. No significant difference was observed between low avoidance-motivated negative condition and neutral condition. Our results are discussed in relation to efficiency processing theory and motivational dimensional model of affect. We conclude that negative emotional states with high avoidance-motivational intensity impair the manipulation process of verbal and spatial working memory.