The dependence of the morphology of neat chloroaluminum phthalocyanine (ClAlPc) films on substrate temperature (Tsub) during deposition is investigated by variable angle spectroscopic ellipsometry (VASE), x-ray diffraction (XRD), and atomic force microscopy (AFM) to obtain detailed information about the molecular orientation, phase separation, and crystallinity. AFM images indicate that both grain size and root mean square (RMS) roughness noticeably increase with Tsub both in neat and blend films. Increasing Tsub from room temperature to 420 K increases the horizontal orientation of the ClAlPc molecules with an increase of the mean molecular tilt angle from 60.13° (300 K) to 65.86° (420 K). The UV-vis absorption band of the corresponding films increases and the peak wavelength slightly red shifts with the Tsub increase. XRD patterns show a clear diffraction peak at Tsub over 390 K, implying the π-stacking of interconnected ClAlPc molecules at high Tsub. Planar and bulk heterojunction (BHJ) photovoltaic cells containing pristine ClAlPc films and ClAlPc:C60 blend films fabricated at Tsub of 390 K show increases in the power conversion efficiency (ηPCE) of 28% (ηPCE = 3.12%) and 36% (ηPCE = 3.58%), respectively, relative to devices as-deposited at room temperature. The maximum short circuit current in BHJs is obtained at 390 K in the Tsub range from 300 K to 450 K.