An in vitro study was conducted to observe the influence of heat treatment on physico-chemical properties of camel milk versus buffalo milk. The experiment was designed with 2× 4 factorial arrangements where in two categories of milk (camel and buffalo) were treated with four thermal treatments (Ambient temperature/no heat treatment, low temperature long time (LTLT), high temperature short time (HTST) and 90ºC for 10min). Two-way interaction of treatment variables was recorded to observe the significant impact of treatments over dependent variables (Physico-chemical). Experiment was replicated three times each in duplicate batches to observe the statistical differences among the variables. Results revealed that compared to buffalo milk, camel milk was more acidic and low in specific gravity, viscosity, conductivity and refractive index. Thermal treatments (Ambient temperature, LTLT, HTST and 90ºC for 10min) applied to both types of milk gradually increased the acidity, viscosity and conductivity, and decreased the specific gravity and refractive index with increase in thermal temperature. Raw camel milk was found rich in protein SNF, ash and casein contents, and poor in total solids, fat, non-casein nitrogen, non-protein nitrogen and whey protein contents against buffalo milk. Linear decrease in lactose, SNF, Non-casein nitrogen (NCN), non-protein nitrogen (NPN) and whey protein contents and increase in Total solids (TS), fat, protein and casein contents was recorded with increase in thermal temperature (Ambient temperature, LTLT, HTST and 90ºC for 10min). Moreover, the increase in denaturation percent in camel milk was observed with increase in heat treatment, but the extent was not comparable with buffalo milk.