A self-consistent atomistic simulation method is established to investigate carbon nanotubes (CNTs) as the charge sensing channels in nonvolatile memory and sensor applications. The theoretical simulation agrees with the experimental results, demonstrating that the sensor can achieve a high sensitivity down to a single electron charge at room temperature. The electrical response of the CNT charge sensor strongly depends on the position of discrete sensing charges even under low drain biases due to the near ballistic transport and quantum interference in a submicron meter CNT channel. This result differs from those for conventional complementary metal-oxide semiconductor charge-based sensors, in which the carrier transport is diffusive and the electrical response is expected to be insensitive to the position variation of the sensing charges. The high sensitivity and nonlinearity of CNT charge-based sensors are important features that need to be considered in the design of CNT memories and sensors.