Porous metal-organic-frameworks (MOFs) are attractive materials for gas storage, separations, and catalytic reactions. A challenge exists, however, on how to introduce larger pores juxtaposed with the inherent micropores in different forms of MOFs, which would enable new functions and applications. Here we report the formation of heterogeneous pores within MOF particles, patterns, and membranes, using a discriminate etching chemistry, called silver-catalyzed decarboxylation. The heterogeneous pores are formed, even in highly stable MOFs, without altering the original structure. A decarboxylated MOF membrane is shown to have pH-responsive switchable selectivity for the flow-assisted separation of similarly sized proteins. We envision that our method will allow the use of heterogeneous pores for massive transfer and separation of complex and large molecules, and that the capability for patterning and positioning heterogeneous MOF films on diverse substrates bodes well for various energy and electronic device applications.