This study investigated the levels of highly toxic pesticides (HTPs) in 6554 vegetable and fruit samples from 31 regions of China, along with the associated risk of dietary exposure for the population between 2014 and 2017. 18 HTPs were detected in 325 (4.96%) samples, and the levels of HTPs in 103 (1.57%) samples were found to be higher than the maximum residue limits (MRLs) of China. The rate of detection of HTPs in six types of vegetables and fruits, in a decreasing order, was found to be as follows: eggplant (8.84%) >grape (5.58%) >tomato (5.43%) >cucumber (5.43%) >pear (3.12%) >apple (2.30%). The level of contamination of HTPs was found to be higher in vegetables compared with fruits. The vegetable and fruit samples with the highest percentages of HTPs exceeding MRLs were found in eggplants from Guangxi (20%) and grapes from Inner Mongolia (12.5%), respectively. Both, the average target hazard quotient (THQ) of a single highly toxic pesticide (HTP) and the average hazard index (HI) of the mixture of HTPs for adults and children from vegetables and fruits from the 31 regions were found to be less than one. Omethoate, carbofuran, ethoprophos, triazophos, and phorate were identified as the major contributors to the average HI for vegetables, and carbofuran, ethoprophos, omethoate, phorate, and phosphamidon were identified as the primary contributors to the average HI for fruits. The results of this study revealed that HTPs in vegetables and fruits did not cause any significant chronic risk of dietary exposure. The detection of HTPs exceeding MRLs in some of the samples implied that appropriate management guidelines for HTPs should be implemented to protect the health of the consumers.