The optical properties of disperse red 1 (DR1) dye molecules can be changed by controlling the molecular configurations using AlPO4-5 (AFI) and SAPO-47 (CHA) single crystals. Polarized and temperature dependent absorption spectra show that DR1 molecules exist as cis configuration in the cages of CHA crystals. The absorption band for cis-configuration is centered at 432 nm, which does not depend on polarization angle and temperature. However, DR1 molecules are well aligned in the channels of AFI crystal with trans configuration. Its absorption band is centered at 520 nm, which shows strongly anisotropic polarizability and shifts to long wavelength with increasing temperature. It can be used as polarizer and temperature sensor. The second harmonic generation (SHG) and photoluminescence (PL) investigations show that the DR1 trans isomers in AFI matrix have potential applications in nonlinear optics.