Thin film Mo–Se–Ni–C coatings for tribologycal applications were prepared by pulsed laser co-deposition from two targets — MoSe2(Ni) and graphite. Two methods of deposition from the MoSe2(Ni) target were used: deposition with unhindered expansion of the laser plume (standard PLD) and deposition of a plume scattered in collisions with Ar gas (pressure 2Pa) in the shadow of a mask (shadow-masked PLD — SMPLD). Doping with carbon by PLD was used in all cases, and carbon content in the composite Mo–Se–Ni–C coatings was varied in the range 35–85.5at.%. Pure MoSex(Ni) coatings were also prepared by PLD and SMPLD. Rutherford backscattering spectroscopy of helium ions, scanning electron and atomic force microscopy, electron probe microanalysis, transmission electron microscopy and micro-diffraction, micro-Raman spectroscopy, X-ray photoelectron spectroscopy and hardness evaluation were all used for comparative studies of the coatings obtained by PLD and SMPLD/PLD. In the PLD coatings, micron-sized particles were found, consisting of pure Ni or MoSe2, as well as nanometre-sized particles of monocrystalline Mo. The nanoparticles were distributed on the surface and in an amorphous matrix in all PLD coatings. Within the amorphous matrix of the Mo–Se–Ni–C coatings, local ordering of atoms was detected, causing the formation of a mixture of amorphous carbon, Mo–C, and Mo–Se phases. Increasing the carbon content caused an increase in the content of sp3 bonds in the carbon phase, and an increase in the hardness of the coatings. SMPLD/PLD coatings had no micro- and nanoparticles, but these coatings were characterized by high selenium content and reduced density. Doping with carbon in the SMPLD/PLD configuration caused the formation of composite coatings containing Mo–Se and amorphous carbon phases as in the PLD coatings, but the hardness of the composite SMPLD/PLD coatings was significantly lower than even the hardness of the pure PLD MoSex(Ni) coatings.