Melanoidins from real foods and model systems have received considerable interest due to potential health benefits. However, due to the complexity of these compounds, to date, the exact structure of melanoidins and mechanism involved in their biological activity has not been fully elucidated. Thus, the aim of this study was to investigate the total phenolic content, antioxidant properties, and structural characteristics of high-molecular weight (HMW) melanoidin fractions isolated by dialysis (>12.4 kDa) from raw and roasted cocoa beans of Criollo, Forastero, and Trinitario beans cultivated in various area. In vitro antioxidant properties of all studied HMW cocoa fractions were evaluated by four different assays, namely free radical scavenging activity against DPPH● and ABTS●+ radicals, ferric reducing antioxidant power (FRAP), and metal-chelating ability. Additionally, the structure-activity relationship of isolated HMW melanoidin fractions were analyzed using attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR). The results show that roasting at a temperature of 150 °C and a relative air humidity of 0.3% effectively enhances the total phenolics content and the antioxidant potential of almost all HMW cocoa melanoidin fractions. The ATR-FTIR analysis revealed that the various mechanisms of action of HMW melanoidins isolates of different types of cocoa beans related to their structural diversity. Consequently, the results clearly demonstrated that HMW cocoa fractions isolated from cocoa beans (especially those of Criollo variety) roasted at higher temperatures with the lower relative humidity of air possess high antioxidant properties in vitro.