This study investigated the time effect of cooperative games on students' emotions of learning science and the treatment effect on their chemistry achievement. This quasi-experimental study compared the use of cards, board games, and riddles, and the use of conventional paper-and-pencil exercises to learn the basics of chemical elements and compounds, for a duration of 4 weeks. One hundred and fourteen ninth graders at an urban public high school in Taipei were involved. The results revealed that the experimental group had significantly higher positive emotion and lower negative emotion throughout the intervention period. While no time effect was observed for the experimental group, a significant time effect on positive and negative emotions in the comparison group using exercises was found: high achievers decreased their positive emotion, and middle to high achievers increased their negative emotion. Furthermore, low and middle achievers performed better when using games. However, no significant difference for the high achievers of the two groups was discovered. This study showed that conventional exercises were detrimental to middle and high achievers' learning emotions, although their concepts improved. Science teachers may try innovative activities such as collaborative games to maintain students' positive emotions and facilitate low achievers' conceptual learning.