This paper proposes a speech rhythm-based method for speaker embeddings to model phoneme duration using a few utterances by the target speaker. Speech rhythm is one of the essential factors among speaker characteristics, along with acoustic features such as F0, for reproducing individual utterances in speech synthesis. A novel feature of the proposed method is the rhythm-based embeddings extracted from phonemes and their durations, which are known to be related to speaking rhythm. They are extracted with a speaker identification model similar to the conventional spectral feature-based one. We conducted three experiments, speaker embeddings generation, speech synthesis with generated embeddings, and embedding space analysis, to evaluate the performance. The proposed method demonstrated a moderate speaker identification performance (15.2% EER), even with only phonemes and their duration information. The objective and subjective evaluation results demonstrated that the proposed method can synthesize speech with speech rhythm closer to the target speaker than the conventional method. We also visualized the embeddings to evaluate the relationship between the distance of the embeddings and the perceptual similarity. The visualization of the embedding space and the relation analysis between the closeness indicated that the distribution of embeddings reflects the subjective and objective similarity.