In this paper, we propose an end-to-end trainable system for recognizing handwritten chemical formulae. This system recognize once a time a chemical formula, instead of one chemical symbol or a whole chemical equation, which is in line with people's writing habits, at the same time could help to develop methods for the complicated chemical equations recognition. The proposed system adopts the CNN+RNN+CTC framework, which is one of state of the art methods in imagebased sequence labelling tasks. We extend the capability of the CNN+RNN+CTC framew...