The development of a miniaturized and low-cost platform for the simultaneous and high-sensitive detection of the nervous system metabolites has gained great interest for early diagnosis and prognostic monitoring of some diseases. Herein, a three-dimensional (3D) interpenetrating hydrogel ink synthesized through a simple hydrothermal assembly way was utilized for the sensitive detection of dopamine released from neural cells in vivo. Carbon nanotubes (CNTs) were utilized as the structural framework, while reduced graphene nanosheets were employed as the outer covering, resulting in the formation of a “skeleton/skin” structure. The attachment of hydrophilic IL molecules onto the graphene nanosheets confers distinctive hydrophilic traits on the resulting nanocomposite material. Consequently, this facilitates its effortless conversion into freestanding paper-like material via printing. The modified electrode was proved to be efficient in electrochemical detection of dopamine by means of DPV, despite the existence of interfering substances like ascorbic and uric acid. With a sensitivity of 41.86 μA μM−1 cm−2 and a low detection limit of 2 nM (S/N = 3), the paper electrode exhibited a linear response ranging from 0.01 to 50 μM. Furthermore, the rGO-CNT-IL was used to determine dopamine levels in the neural cells. The modified paper electrode can also be potentially applied for further drug detection, health monitoring and other biological applications.