Magnetism in the two-dimensional limit has become an intriguing topic for exploring new physical phenomena and potential applications. Especially, the two-dimensional magnetism is often associated with novel intrinsic spin fluctuations and versatile electronic structures, which provides vast opportunities in 2D material research. However, it is still challenging to verify candidate materials hosting two-dimensional magnetism, since the prototype systems have to be realized by using mechanical exfoliation or atomic layer deposition. Here, an alternative manipulation of two-dimensional magnetic properties via electrochemical intercalation of organic molecules is reported. Using tetrabutyl ammonium (TBA<sup>+</sup>), we synthesized a (TBA)Cr<sub>2</sub>Ge<sub>2</sub>Te<sub>6</sub> hybrid superlattice with metallic behavior, and the Curie temperature is significantly increased from 67 K in pristine Cr<sub>2</sub>Ge<sub>2</sub>Te<sub>6</sub> to 208 K in (TBA)Cr<sub>2</sub>Ge<sub>2</sub>Te<sub>6</sub>. Moreover, the magnetic easy axis changes from the ⟨001⟩ direction in Cr<sub>2</sub>Ge<sub>2</sub>Te<sub>6</sub> to the <i>ab</i>-plane in (TBA)Cr<sub>2</sub>Ge<sub>2</sub>Te<sub>6</sub>. Theoretical calculations indicate that the drastic increase of the Curie temperature can be attributed to the change of magnetic coupling from a weak superexchange interaction in pristine Cr<sub>2</sub>Ge<sub>2</sub>Te<sub>6</sub> to a strong double-exchange interaction in (TBA)Cr<sub>2</sub>Ge<sub>2</sub>Te<sub>6</sub>. These findings are the first demonstration of manipulation of magnetism in magnetic van der Waals materials by means of intercalating organic ions, which can serve as a convenient and efficient approach to explore versatile magnetic and electronic properties in van der Waals crystals.