Calcium carbonate (CaCO)-based nanoadsorbents have gained widespread attention due to their superiority in removing toxic heavy metal ions. Considering that the inherent structure of the material determines its performance, it is important to fully understand the effect of different crystals of CaCO on the removal of heavy metals. On the other hand, the difficult separation of nanoadsorbents during in situ remediation may cause the potential risk of secondary pollution by the remaining adsorbents. Herein, the magnetic calcium carbonate adsorbents with nanostructure (MCCR-X, X represent the annealing temperature) were fabricated with a tunable crystal structure of CaCO by adjusting the annealing temperature. Results from batch experiments revealed the crystal structure (CaCO)-dependent adsorption performance of MCCRs toward Pb(II) and Cd(II). MCCR-350 with an aragonite phase showed the outstanding adsorption toward both Pb(II) and Cd(II) with maximum adsorption capacity of 1179 and 821 mg/g, and MCCR-RAW with a vaterite/aragonite phase also has similar adsorption properties. However, MCCR-550 with the calcite phase displayed a superhigh adsorption toward Pb(II) only but very weak adsorption toward Cd(II) with a capacity of 1350 and 30 mg/g in the initial concentration of 300 mg/g. The findings indicated that the efficiently tunable removal of the heavy metal ion Pb(II) or Cd(II) by MCCRs can be realized by regulating the crystal phase of CaCO. X-ray photoelectron spectroscopy technology (XPS) was employed to clarify the possible mechanism of the crystal phase of CaCO-dependent adsorption ability for Pb(II)/Cd(II) removal by MCCRs. This work provides an understanding of the crystal-structure-related adsorption properties of CaCO and also gives guidance for designing a CaCO-based adsorbent for removal/recovery of heavy metal ions.