An approach of implementing X-bar and R control charts as a statistical control tool to monitor the changes in the melting profile of fresh and stored flaxseed oils by differential scanning calorimetry (DSC) was used. Phase transition melting profiles were collected after 0, 2, 4, and 6 months of storing flaxseed oils, originating from five different cultivars. Four peaks at around −36, −30, −25, and −12 °C were identified using the deconvolution analysis procedure, which enabled the data to be collected at peak temperature (T), peak height (h), the peak area (A), and the percentages of the area (P A), as well as the ratio calculated from these parameters. Control charts obtained for the second peak of the melting profile showed a significant decrease of peak height (h2) from 0.50 to 0.39 W/g and the percentage of the area (P A2) from 50 to 38%, within the storage time (p ≤ 0.05); thus, they were considered to be indicators of oil deterioration. Strong negative correlations of the unstable parameters of DSC with chemical indicators of the oils’ oxidative stability (PV, p-AV, TOTOX) were found. For DSC parameters, related to the first peak (h1, A1) and the third peak (h3, A3), changes were statistically not significant within storage (p > 0.05); thus, they can be used as markers of flaxseed oil authenticity. The study demonstrated that X-bar and R control charts could effectively monitor changes in the specific peaks and calculated ratios from the DSC melting profile of fresh and stored flaxseed oils, serving as reliable indicators of oil deterioration.