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Abstract The ultrafast monitoring of deoxyribonucleic acid (DNA) dynamic structural changes is an emerging and rapidly growing research topic in biotechnology. The existing optical spectroscopy used to identify different dynamical DNA structures lacks quick response while requiring large consumption of samples and bulky instrumental facilities. It is highly demanded to develop an ultrafast technique that monitors DNA structural changes with the external stimulus or cancer‐related disease scenarios. Here, we demonstrate a novel photonic integrated graphene‐optofluidic device to monitor DNA structural changes with the ultrafast response time. Our approach is featured with an effective and straightforward design of decoding the electronic structure change of graphene induced by its interactions with DNAs in different conformations using ultrafast nanosecond pulse laser and achieving refractive index sensitivity of ~3 × 10−5 RIU. This innovative technique for the first time allows us to perform ultrafast monitoring of the conformational changes of special DNA molecules structures, including G‐quadruplex formation by K+ ions and i‐motif formation by the low pH stimulus. The graphene‐optofluidic device as presented here provides a new class of label‐free, ultrafast, ultrasensitive, compact, and cost‐effective optical biosensors for medical and healthcare applications.