In order to clarify the ecological and biological effects of fruit bagging, tomato variety JYK was taken as the test material to study the changes of the microenvironment in different color fruit bags and the effects of these changes on the fruit development, yield and quality, with the treatment without fruit bagging as the control (CK). The results showed that bagging with different color fruit bags had positive effects in decreasing the light intensity of the microenvironment and increasing its temperature and humidity, and thus, increased the single fruit mass and promoted the harvest stage advanced. Black bag had the best effects in increasing microenvironment temperature and fruit mass, with the single fruit mass increased by 27.2% and the harvest period shortened by 10 days, compared with CK. The fruit maturation period in colorless bag, blue bag and red bag was shortened by 8, 3 and 2 days, and the single mass was increased by 11.8%, 6.4% and 4.8%, respectively. Moreover, the coloring and lycopene content of the fruits with different color bags bagging were improved, but the fruit rigidity and fruit soluble solid, soluble protein, and soluble sugar contents were decreased. Therefore, bagging with different color bags could improve the yield of tomato fruits, but decrease the fruit nutritional quality.