Lanthanide-based upconversion molecular complexes have potential application in diverse fields and attracted considerable research interest in recent years. However, the similar coordination reactivity of lanthanide ions has constrained the designability of target molecule with well-defined structure, and many attempts obtained statistical mixtures. Herein, an ion-paired Yb-Eu heteronuclear complex [Eu(TpPy)2][Yb(ND)4] (TpPy = tris[3-(2-pyridyl)pyrazolyl]hydroborate, ND = 3-cyano-2-methyl-1,5-naphthyridin-4-olate) was designed and synthesized. Thanks to the radius difference between Eu3+ (1.07 Å) and Yb3+ (0.98 Å) ions, the hexadentate TpPy ligand was selected to coordinate with Eu3+ and the Yb3+ with a smaller radius was chelated by bidentate ND ligand. As a result, the sites of Eu3+ and Yb3+ in the complex can be clarified by high-resolution mass spectrometry and single-crystal structure analysis. Upon the excitation of Yb3+ at 980 nm, the upconversion emission of Eu3+ was realized through a cooperative sensitization process. Furthermore, [Eu(TpPy)2][Yb(ND)4] demonstrated excellent photostability during continuous high-power density 980 nm laser irradiation, with a LT95 (the time to 95% of the initial emission intensity) of 420 minutes. This work provides the first example of a pure ion-paired Yb-Eu heteronuclear complex upconversion system and may bring insights into rational design of lanthanide-based upconversion molecular complexes.