Recently, it was shown that the spectrum of anomalous dimensions and other important observables in planar N=4 supersymmetric Yang-Mills theory are encoded into a simple nonlinear Riemann-Hilbert problem: the Pμ system or quantum spectral curve. In this Letter, we extend this formulation to the N=6 supersymmetric Chern-Simons theory introduced by Aharony, Bergman, Jafferis, and Maldacena. This may be an important step towards the exact determination of the interpolating function h(λ) characterizing the integrability of this model. We also discuss a surprising relation between the quantum spectral curves for the N=4 supersymmetric Yang-Mills theory and the N=6 supersymmetric Chern-Simons theory considered here.