Recurrent changes of temperature and persistence of cooling along fingers at the room temperature make hands the most frequent region of interest for thermography in systemic sclerosis (SSc). The aim of this study was to evaluate dependance of temperature in hands on a subtype of the disease, immune profile of antinuclear antibodies (ANA), and lung involvement. There were 29 patients with limited cutaneous involvement (lcSSc) and 10 patients with diffuse cutaneous disease (dcSSc) enrolled for the study. To compare measurements to normal values, there were enrolled 29 healthy volunteers (control group). All participants were submitted to thermography with handheld camera FLIR One Pro for iOS, attached to mobile phone iPhone 11, at the fixed temperature of 21 °C. Measurements included average temperature (T) over nailfolds in thumbs and fingers II-V, as well as the difference in average temperatures (TΔ) between metacarpus of the hand and its thumb and fingers II-V. Both thumbs and fingers II-V remained cooler in subjects with dcSSc compared to those with lcSSc. This implicated a significantly greater TΔ along thumbs and fingers II-V in dcSSc group. Although T at nailfolds in SSc patients was not lower than in healthy controls, TΔ remained significantly more pronounced in both lcSSc and dcSSc subjects. A positivity to ACA in lcSSc group was found to be associated with significantly lower T and more pronounced TΔ in fingers II-V than the presence of anti-Scl70 antibodies. Temperature measurements remained statistically independent on a presence of ILD in lcSSc group, but both thumbs and fingers II-V in dcSSc group were warmer in case of lung involvement. The study showed the dcSSc subtype, the positivity of ACA in lcSSc, but not lung involvement were associated with poorer thermal control in the hands of SSc patients. A comparison to healthy controls highlighted the weakness of temperature measurements at nailfolds (T) but increased the value of TΔ in thermography of hands.