The BRI has put new drive into China’s relations with Kyrgyzstan. The three years since the launch of the BRI have witnessed substantial achievements in the China-Kyrgyzstan Economic Corridor，with bilateral economic cooperation taking up a new look. Amid the achievements and complicated geopolitical situation，China-Kyrgyzstan Economic Corridor still faces serious potential problems. Though not posing grave threat to the overall economic cooperation of the two countries，these potential problems may give rise to ups and downs to China-Kyrgyzstan economic cooperation and the overall unfolding of the BRI，if proper attention and measures are not given. Based on above-mentioned consideration，this article makes an in-depth analysis of the security risks facing the development program connection，economic corridor，and cross-border passage before producing targeted measures to ensure the smooth progress of China-Kyrgyzstan Economic Corridor.