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Based on the idea that there is no side channel in the vacuum state, the side-channel-free quantum key distribution (SCFQKD) protocol was proposed, which is immune to all attacks in the source side-channel space and all attacks in the detectors. In the original SCFQKD protocol, an important assumption is that Alice and Bob can produce the perfect vacuum pulses. But due to the finite extinction ratio of the intensity modulators, the perfect vacuum pulse is impossible in practice. In this paper, we solve this problem and make the quantum key distribution side-channel secure with real source device which does not emit perfect vacuum pulses. Our conclusion only depends on the upper bounds of the intensities of the sources. No other assumptions such as stable sources and stable side channels are needed. The numerical results show that, comparing with the results of SCFQKD protocol with perfect vacuum sources, the key rates and secure distance are only slightly decreased if the upper bound of the intensity of the imperfect vacuum source is less than $10^{-8}$ which can be achieved in experiment by two-stage intensity modulator. We also show that the two-way classical communication can be used to the data post-processing of SCFQKD protocol to improve the key rate. Specially, the active odd-parity pairing method can improve the key rates in all distances by about two times and the secure distance by about 40 km. Give that the side channel security based on imperfect vacuum, this work makes it possible to realize side channel secure QKD with real devices.