We present a scheme that is capable of detecting photon numbers during the quantum key distribution (QKD) based on an improved differential phase shift (DPS) system without Trojan horse attack. A time-multiplexed detector (TMD) is set in for the photon-number resolution. Two fibre loops are used for detecting photon numbers as well as distributing keys. The long-term stabilization is guaranteed by two Faraday mirrors (FM) at Bobs site to automatically compensate for polarization defect. Our experimental study (90km QKD is completed) indicates that such a system is stable and secure which nearly reaches the performance of a single photon scheme.