Multimodal imaging can provide multidimensional information for understanding concealed microstructures or bioprocesses in biological objects. The combination of over-1000 nm near-infrared (OTN-NIR) fluorescence imaging and magnetic resonance (MR) imaging is promising in providing high sensitivity and structural information of lesions. This combination can be facilitated by the development of an imaging probe. The OTN-NIR and MR bimodal fluorescence probes reported to date primarily involve ceramic particles for fluorescence and MRI contrast enhancement effect. In this study, we designed a new bimodal OTN-NIR/MR imaging probe from organic components including an OTN-NIR fluorescent organic dye (IR-1061) encapsulated in the core of a micelle composed of poly(lactic-co-glycolic acid)-block-poly(ethylene glycol) copolymer (PLGA-PEG). For the MRI contrast, gadobutrol (Gd-DOTA) was introduced at the end of the PEG chain at various ratios. Thereafter, the OTN-NIR fluorescence and MR bimodal imaging probes of ca. 20 nm in size were successfully prepared and applied in mouse imaging. The probe exhibited absorption and emission in the OTN-NIR, and T1 contrast enhancement effects on MRI. Moreover, it demonstrated bright OTN-NIR fluorescence and MRI contrast enhancement to depict veins and observe the organs in live mice. The imaging results revealed that the Gd-DOTA introduction ratio is of great importance for controlling the biological response of the probe without reducing the contrast enhancement effect.