Numerous toxicological and epidemiological studies have shown that microcystin-LR (MC-LR) could cause a variety of toxicity to humans and animals. However, the absence of effective methods to trace MC-LR in biological systems has hindered the in-depth understanding of the mechanism of MC-LR toxicity. Near-infrared (NIR) fluorescent probes are crucial tools for accurate visualization and in-depth study of specific molecules in biological systems. Due to the lack of effective design strategies, NIR fluorescent probes for imaging MC-LR specifically in biological systems have not been reported yet. In order to address this pressing issue, herein, we have introduced a new and facile strategy to improve MC-LR detection and imaging in biological systems, and based on this design strategy, three NIR fluorescence probes (MC-RdTPA1, MC-RdTPA2, and MC-RdTPE1) have been constructed. These probes have several advantages: (i) have long emission wavelength and large Stokes shifts, which have great potential in vivo imaging applications; (ii) could selectively visualize MC-LR in cells; and (iii) showed stable fluorescence intensity in the pH range of 5.0-7.0. This work may provide a new avenue for the detection of MC-LR in biological systems and new tool to advance our knowledge of the mechanism of MC-LR toxicity.