Electrocardiogram (ECG) signal based cross-subject emotion recognition methods reduce the influence of individual differences using domain adaptation (DA) techniques. These methods generally assume that the entire unlabeled data of unknown target subjects are available in training phase. However, this assumption does not hold in some practical scenarios where the data of target subjects arrive one by one in an online manner instead of being acquired at a time. Thus, existing DA methods cannot be directly applied in this case since the unknown target data is inaccessible in training phase. To tackle the problem, we propose a novel online cross-subject ECG emotion recognition method leveraging hypergraph-based online transfer learning (HOTL). Specifically, the proposed hypergraph structure is capable of learning the high-order correlation among data, such that the recognition model trained on source subjects can be more effectively generalized to target subjects. Meanwhile, the structure can be easily updated by adding a hyperedge which connects a newly coming sample with the current hypergraph, resulting in further reduce the individual differences in online manner without re-training the model. Consequently, HOTL can effectively deal with the online cross-subject scenario where unknown target ECG data arrive one by one and varying overtime. Extensive experiments conducted on the Amigos dataset validate the superiority of the proposed method.