The present invention provides a fluorine-containing elastomer composition containing a particular filler, and a molded article excellent in heat resistance obtained by crosslinking the composition. The present invention also provides a process for preparing a fluorine-containing elastomer composition comprising a step of preparing a surface-treated filler by treating a surface of a filler with a hydrophobic treatment agent so as to have a hydrophobization degree of at least 30% which is measured by the particular method. The present invention relates to a fluorine-containing elastomer composition comprising at least one kind of a crosslinking agent selected from the group consisting of an oxazole crosslinking agent, an imidazole crosslinking agent, a thiazole crosslinking agent and a triazine crosslinking agent, a fluorine-containing elastomer having a crosslinking site capable of a crosslinking reaction with the crosslinking agent, and a surface-treated filler in which a hydrophobization degree of the surface-treated filler is at least 30% which is measured by a particular method.