We report on Raman sideband cooling of 25 Mg þ to sympathetically cool the secular modes of motion in a 25 Mg þ -27 Al þ two-ion pair to near the three-dimensional (3D) ground state. The evolution of the Fock-state distribution during the cooling process is studied using a rate-equation simulation, and various heating sources that limit the efficiency of 3D sideband cooling in our system are discussed. We characterize the residual energy and heating rates of all of the secular modes of motion and estimate a secular motion time-dilation shift of −ð1.9 AE 0.1Þ × 10 −18 for an 27 Al þ clock at a typical clock probe duration of 150 ms. This is a 50-fold reduction in the secular motion time-dilation shift uncertainty in comparison with previous 27 Al þ clocks. DOI: 10.1103/PhysRevLett.118.053002 Trapped and laser-cooled ions are useful for many applications in quantum information processing and quantum metrology because of their isolation from the ambient environment and the mutual Coulomb interaction [1][2][3][4][5][6]. The Coulomb interaction establishes normal modes of motion, called secular modes, which enable information exchange and entanglement between ions. For many operations in quantum information processing and metrology, these secular modes should, ideally, be prepared in their ground state. For example, in state-of-the-art trappedion optical clocks [7], uncertainty in the Doppler shift due to the residual excitation of these modes is a dominant contribution to the total clock uncertainty [8][9][10].All trapped-ion optical clocks to date have been operated with the ions' motion near the Doppler cooling limit [7][8][9][10]. For clocks based on quantum-logic spectroscopy of the 1 S 0 ↔ 3 P 0 transition in 27 Al þ [11], the smallest uncertainty has been achieved by performing continuous sympathetic Doppler cooling on the logic ion ( 25 Mg þ ) during the clock interrogation [8]. Because of the difficulty of performing accurate temperature measurements of trapped ions near the Doppler cooling limit, the uncertainty of the secular motion temperature was limited to 30% [8].To reduce the secular motion time-dilation shift and its uncertainty, sub-Doppler cooling techniques can be employed [12][13][14][15][16][17]. These schemes have not previously been implemented in ion-based clock experiments due to high ambient motional heating rates, the need for extra cooling laser beams, and the difficulty of characterizing the resulting motional state distribution, which can be nonthermal [8,10,18]. For example, in sideband cooling, a nonthermal distribution can result from zero crossings in the cooling transition Rabi rate as a function of the Fock state [19,20] and from cooling durations insufficient to reach equilibrium. Although sideband cooling can reach extremely low energies, a small nonthermal component of the distribution may contribute more than 90% of the total energy [21], rendering the temperature measurement technique using motional sideband ratios unsuitable for determining the energy [12,13].Here, we dem...