While chemically and thermally modified citrus pectin (MCP) has already been studied for health benefits, it is unknown how size-fractionated oligo- and polysaccharides differentially affect cancer cell behavior. We produced thermally MCP and fractionated it by molecular size to evaluate the effect these polymers have on cancer cells. MCP30/10 (between 30 and 10 kDa) had more esterified homogalacturonans (HG) and fewer rhamnogalacturonans (RG-I) than MCP and MCP30 (higher than 30 kDa), while MCP10/3 (between 10 and 3 kDa) showed higher amounts of type I arabinogalactans (AGI) and lower amounts of RG-I. MCP3 (smaller than 3 kDa) presented less esterified HG and the lowest amount of AGI and RG-I. Our data indicate that the enrichment of de-esterified HG oligomers and the AGI and RG-I depletions in MCP3, or the increase of AGI and loss of RGI in MCP30/10, enhance the anticancer behaviors by inhibiting migration, aggregation, and proliferation of cancer cells.