Reduced flow-rate electrospray ionization has been proven to provide improved sensitivity, less background noise, and improved limits of detections for ESI-MS analysis. Miniaturizing the ESI source from conventional electrospray to micro-electrospray and further down to nanoelectrospray has resulted in higher and higher sensitivity. However, when effects of flow rate were investigated for atmospheric pressure ESI-IMS using a nanospray emitter, a striking opposite result was observed. The general tendency we observed in ESI-IMS was that higher flow rate offered higher ion signal intensity throughout a variety of conditions investigated. Thus further efforts were undertaken to rationalize these contradictory results. It is well accepted that decreased flow rate increases both ionization efficiency and transmission efficiency thus improves ion signal in ESI-MS. However, our study revealed that decreased flow rate results in decreased ion signal because ion transfer is constant no matter how flow rate changes in ESI-IMS. Since ion transfer is constant in atmospheric pressure ESI-IMS, ionization efficiency can be studied independently, which otherwise is not possible in ESI-MS where both ionization efficiency and transmission efficiency vary as conditions alter. In this report, we present a systematic study on signal intensity and ionization efficiency at various experimental conditions using ESI-IMS and demonstrated the ionization efficiency as a function of flow rate, analyte concentration, and solvent composition.