Lysozyme is a rigid globular protein with four disulfide bonds which is present in human tears, saliva, sweat and milk. In the present study, thin films of this protein are deposited on hydrophilic (OH-Si) and hydrophobic (H-Si) silicon surfaces using dip coating method. In order to study the effect of ions these films were also fabricated by varying the concentration of mono-(Na+), di-(Ca2+) and tri-(Y3+) valent ions. The structural and topographical characteristics of these films are investigated using X-ray reflectivity (XRR) and atomic force microscopy (AFM) techniques and are correlated with the surface hydrophobicity/hydrophilicity. On hydrophilic OH-Si surface, a thick layer of lysozyme (≈ 47 Å) is adsorbed in absence of ions. However, in presence of 1-10 mM of ions the thickness varied to ≈ 40 to 61 Å. Conversely, the thickness of the lysozyme film in absence of any ions on hydrophobic H-Si surface is ≈ 57 Å which varied in the range of ≈ 44 to 69 Å in presence of the ions. Mostly, bi-molecular layer is formed on the substrate surface where for the substrate-attached lower layer molecules are in side-on orientation (≈ 24 Å) and on top of that one more layer is formed where the molecules are either in side-on orientation or tilted with respect to the lower layer. On OH-Si surface, pure or ions interacted lysozyme films are adsorbed in its native globular form with almost negligible structural modification. However, on hydrophobic surface, globular shape of adsorbed lysozyme molecules is slightly elongated mostly due to the presence of relatively higher hydrophobic interaction between the protein and H-Si surface. Hydrophobic nature of the protein films as obtained from the contact angle studies showed that on OH-Si surface the contact angle of lysozyme film interacted by Na+ ions is highest, whereas it is intermediate and lowest for Y3+ and Ca2+ ions respectively. Moreover, the contact angle of lysozyme film is highest for Ca2+ and lowest for Na+ ions on H-Si surface. Therefore, the thicker protein films exhibit more hydrophobic nature and the contact angle varies in accordance with the electron density of the adsorbed films.