Membraneless organelles formed by phase-separated nucleic acid or protein condensates play vital roles in regulating cellular functions. Integrating such synthetic organelles into protocell carriers remains a key challenge. Here, we introduce a method to assemble functional phase-separated organelles within liposome protocells. Pre-engineered nucleic acids are encapsulated with ligase in locked-DNA-nanopore modified protocells. Upon nanopore unlocking and Mg²⁺ influx, the constituents ligate into programmable polymer chains that crosslink into barcode-modified condensates. Photoresponsive, caged nucleic acids hybridize with barcode tethers on two distinct organelles, forming a functional two-organelle system in the protocells. Light-induced uncaging releases an information-transfer strand from one organelle, triggering intercommunication and reconfiguration of the partner condensate. By predesigning organelle compositions and transfer strands, the emergence of catalytic DNAzymes or transcriptional machinery in the organelle/protocell assemblies are demonstrated, resulting in dynamic structural reconfiguration of the organelles.