It has been proved that irrigation with high saline water and leaching fraction (LF) affect crop yield, but the effects of irrigation water salinity (ECiw) and LF on fruit quality remain largely elusive. We therefore investigated the effects of ECiw and LF on the yield, fruit quality, and ion content of hot peppers. An experiment using irrigation water with five levels of salinity (ECiw of 0.9, 1.6, 2.7, 4.7, and 7.0 dS·m−1) and two LFs (0.17 and 0.29) was conducted in a rain shelter. The experiment took the form of a completely randomized block design, and each treatment was replicated four times. We increased the salinity of the irrigation water by adding 1:1 milliequivalent concentrations of NaCl and CaCl2 to a half-strength Hoagland solution. The plants were irrigated for 120% and 140% evapotranspiration, corresponding to an LF of 0.17 and 0.29. Results showed that the total fruit yield decreased significantly with an increase in the ECiw as a result of reduction both in the fresh weight of fruit and the number of fruit per plant. An increase in the ECiw also led to a decrease in the total dry biomass of fruit and plant, as well as decreasing water use efficiency (WUEF). Salinity reduced the appearance of the fruit by both decreasing the length (FL) and maximum width (FMW) of the fruit. However, increased ECiw also improved the taste of the hot peppers by increasing the total soluble solid (TSS) content, as well as adding to their nutritional quality with a higher content of Vitamin C (VC). Their storage quality was also improved because of an improvement in the firmness of the fruit (Fn) as well as a reduction in the fruit water content (FWC). An increase in the LF led to an increase in the total fruit yield, total dry biomass of fruit and plant, and WUEF; it also increased the FWC and VC content, and decreased the FMW and fruit shape index (FSI). The threshold-slope linear response and sigmoidal-sharp models were both a good fit for the measured total fruit yield, and the LF had no significant effect on the model parameters. The relative TSS and Fn increased linearly as the electrical conductivity (EC) of soil-saturated paste extract (ECe) increased, whereas they decreased linearly as the relative seasonal evapotranspiration (ETr) increased regardless of the LFs. The relative FW, FL, and FMW decreased linearly with the increased ECe, and increased linearly with the increased ETr regardless of the LFs. The relative fruit Na+ concentration increased linearly as the ECe increased. The regression correlations between the total fruit yield, fruit quality parameters, ion contents, and ECe or ETr could provide important information for salinity and irrigation water management with a compromise between the hot pepper yield and fruit quality.