Citrus Huanglongbing (HLB) is incurable, so it is necessary to develop an accurate and timely detection method for citrus HLB. Volatile organic compounds (VOCs) of plants can be used as an indicator of their health status. Based on the difference of VOCs between healthy and HLB citrus leaves, we designed the polyethyleneimine (PEI)-modified carboxylic multi-walled carbon nanotubes (CNT-COOH) gas sensor and used it in the diagnosis of citrus HLB. Our PEI/CNT-COOH sensor showed significant impedance responses to four citrus HLB biomarkers VOCs (ethylhexanol, phenylacetaldehyde, linalool and methyl salicylate) with sensitivity up to single-digit ppm. We then used the sensor to detect the VOCs in citrus leaves, and found that the diseased citrus can be distinguished from the healthy citrus according to the different response values of the sensor, successfully identified HLB-infected citrus. Compared with the conventional qPCR method, PEI/CNT-COOH sensor not only has higher accuracy, but also can be used in real time field detection of citrus leaves due to its less stringent operating condition and portability.