N2O emissions were measured monthly for 1 year using the static chamber method along the littoral and pelagic zones of Meiliang Bay in hyper-eutrophic Taihu Lake. The results indicated that littoral zones were the “hotspots” of N2O emissions (−278∼2101μgN2Om−2 h−1). While the littoral zone accounted for only 5.4% of the area of Meiliang Bay, the N2O emissions from the littoral zones were about 43.6% of total emissions from the bay. The importance of spatial variation on N2O emissions was demonstrated by dividing the lake into four unique zones through cluster analysis. The eulittoral zone was the key area of N2O emissions with an annual 5% trimmed mean 429.5μgN2Om−2 h−1, following by supralittoral (138.8μgN2Om−2 h−1), infralittoral (98.9μgN2Om−2 h−1), and pelagic zones (15.7μg N2Om−2 h−1). Further, N2O emissions showed a seasonal trend. Excessive N2O emissions during algal bloom periods suggested that algae played a significant role in the emission of N2O.