Based on the widespread distribution and abundant phytoliths produced by Phragmites communis, phytoliths of P. communis in northeast China were investigated to identify the primary influencing factors on phytolith size using an orthogonal experimental method. Temperature and precipitation were found to be the prominent factors influencing the sizes of short-cell phytoliths including the saddle and the rondel morphotypes, whereas there were no obvious variations in the width-to-length ratios of short-cell phytoliths in response to environmental factors. These results indicate that short-cell phytoliths are genetically stable, confirming that they can be used for the classification of grasses. Moreover, precipitation was the main factor influencing the sizes of the lanceolate phytoliths and silicified stomata, and their width-to-length ratios changed significantly in response to precipitation and habitat differences. These findings reveal that lanceolate and silicified stomata phytoliths are sensitive to environmental changes, indicating their usefulness for palaeoenvironment reconstruction. Moreover, variations in their width-to-length ratios and their sizes may provide some information for plant classification, even at species level. Finally, the results of a principal component analysis of the sizes of P. communis phytoliths further verify the reliability of the orthogonal experiment results, in that temperature and precipitation were the prominent factors influencing the size of all P. communis phytoliths except for the length of saddle and width of the saddle morphotypes. This research into the primary environmental significance of the sizes of P. communis phytoliths may contribute to improving the precision of plant classification and the model for quantitative reconstruction of the palaeoenvironment to aid in reconstructions of palaeovegetation and palaeoclimate.