In this work, we report on the synthesis, in-depth crystal structure studies as well as optical and magnetic properties of newly synthesized heterometallic quaternary selenides of the Eu+2Ln+3Cu+1Se3 composition. Crystal structures of the obtained compounds were refined by the derivative difference minimization (DDM) method from the powder X-ray diffraction data. The structures are found to belong to orthorhombic space groups Pnma (structure type Ba2MnS3 for EuLaCuSe3 and structure type Eu2CuS3 for EuLnCuSe3, where Ln = Sm, Gd, Tb, Dy, Ho and Y) and Cmcm (structure type KZrCuS3 for EuLnCuSe3, where Ln = Tm, Yb and Lu). Space groups Pnma and Cmcm were delimited based on the tolerance factor t’, and vibrational spectroscopy additionally confirmed the formation of three structural types. With a decrease in the ionic radius of Ln3+ in the reported structures, the distortion of the (LnCuSe3) layers decreases, and a gradual formation of the more symmetric structure occurs in the sequence Ba2MnS3 → Eu2CuS3 → KZrCuS3. According to magnetic studies, compounds EuLnCuSe3 (Ln = Tb, Dy, Ho and Tm) each exhibit ferrimagnetic properties with transition temperatures ranging from 4.7 to 6.3 K. A negative magnetization effect is observed for compound EuHoCuSe3 at temperatures below 4.8 K. The magnetic properties of the discussed selenides and isostructural sulfides were compared. The direct optical band gaps for EuLnCuSe3, subtracted from the corresponding diffuse reflectance spectra, were found to be 1.87–2.09 eV. Deviation between experimental and calculated band gaps is ascribed to lower d states of Eu2+ in the crystal field of EuLnCuSe3, while anomalous narrowing of the band gap of EuYbCuSe3 is explained by the low-lying charge-transfer state. Ab initio calculations of the crystal structures, elastic properties and phonon spectra of the reported compounds were performed.