Developing single-particle nanocomposite with aqueous-phase orthogonal multicolor phosphorescence or multimodal luminescence holds great significance for optical coding, anti-counterfeiting encryption, bioimaging, and biosensing. However, it faces challenges such as a limited range of emission wavelengths and difficulties in controlling the synthesis process. In this work, a conjugate structure manipulation integrated luminophor confinement strategy is proposed to prepare carbon dots@upconversion nanoparticles (CDs@UCNPs) featuring aqueous-phase orthogonal multicolor room-temperature phosphorescence-upconversion luminescence (RTP-UCL) through wet-chemical synthetic methods. Four types of CDs are synthesized by introducing molecules with varying degrees of conjugation, while the intersystem crossing process is enhanced by constructing charge-transfer states to narrow the energy gap between the excited singlet and triplet states. Aqueous-phase orthogonal multicolor RTP (green, yellow, and orange) and UCL (blue, green, yellow, and red) are achieved by confining CDs with different conjugation degrees within a NaBiF