To test the target detection accuracy of infrared detectors in practical applications, this study proposes a near space detection (NSD) technology that integrates van der Waals heterojunction photodetectors with long-range infrared target detection algorithms (ITDAs). A van der Waals heterojunction infrared photodetector (MoS2/CdTe) is prepared by combining molybdenum disulfide thin film and cadmium telluride substrate, and depositing gold electrodes on both substrates. A fusion algorithm of spatiotemporal target detection network and local contrast method is proposed for long-distance detection of weak infrared targets, and a near-space infrared detection system is designed. The data showed that the MoS2/CdTe heterojunction photodetector had a detection range of 200–1700 nm and a response of 36.7 mA/W, demonstrating excellent optoelectronic performance. The false alarm rates of the long-distance ITDA were 0.006% and 0.009%, respectively, which are significantly better than the target detection algorithm based on local contrast. In the testing of the near-space infrared detection system, the errors in the shortwave and longwave field of view tests were 2.5% and 5.2%, respectively, and the resolution test errors were 3.6% and 3.7%. The infrared detection system meets the performance standards, has high detection ability and stability, and provides a more effective solution for NSD.