Thermodynamics of the formation of coordination polymers (CPs) or metal-organic frameworks (MOFs) has not been focused on, whereas many CPs or MOFs have been synthesized in a solution. With a view of separating Nd3+ and Dy3+ in an aqueous solution, we demonstrate that crystallization of the CPs of Nd3+ and Dy3+ based on dibutyl phosphoric acid (Hdbp) can be thermodynamically described; crystallization yields of [Ln(dbp)3] (Ln = Nd or Dy) complex are predicted well using a simple calculation, which takes the apparent solubility products (Kspa) for [Ln(dbp)3] and the acid dissociation constant of Hdbp into account. The Kspa values of [Nd(dbp)3] and [Dy(dbp)3] are experimentally determined to be (1.3 ± 0.1) × 10-14 and (2.9 ± 0.4) × 10-18 M4, respectively, at 20 °C. The ratio of these Kspa values, that is, ca. 4500, is significantly larger than the ratio of the solubility products for inorganic salts of Nd3+ and Dy3+. Therefore, Nd3+ and Dy3+ are selectively crystallized in an aqueous solution via the formation of CPs. Under optimized conditions, Dy3+ crystallization is preferable, whereas Nd3+ remains in the solution phase, where the ratio of the Dy molar content to the total metal content (i.e., Nd + Dy) in the crystal is higher than 0.9. The use of acids, such as HCl or HNO3, has no practical impact on the separation in an aqueous solution.