Loss is inevitable for the optical system due to absorption of materials, scattering caused by the defects and surface roughness. In quantum optical circuits, the loss can not only reduce the intensity of signal, but also affect the performance of quantum operations. In this work, we divide losses into unbalanced linear loss and shared common loss, and provide a detailed analysis on how loss affects the integrated linear optical quantum gates. It is found that the orthogonality of eigenmodes and the unitary phase relation of the coupled waveguide modes are destroyed by the loss. As a result, the fidelity of single-and two-qubit operations decrease significant as the shared loss becomes comparable to the coupling strength. Our results are important for the investigation of large-scale photonic integrated quantum information process. OCIS Codes: 130.0130, 270.0270.Photonic integrated circuits [1] (PIC) have been developed for the increasing complexity of both classical and quantum information processing, which is demanding on scalability, stability and high quality interference. By integrating the waveguides and controlling their coupling on a chip, basic optical elements [2] in bulk optics can be realized on-chip with high quality, such as beam splitter (BS), phase shifter and polarization beam splitter (PBS) [3,4] . Recently, quantum C-NOT gate, quantum walk and Boson sampling have been performed on a single chip, based on silica-on-silicon waveguides [5,6] , laser direct writing waveguides [7,8] and plasmonic waveguides [9,10] . While, there still remains challenges to integrate optical devices with good performance, and the errors due to experimental imperfection will be amplified when cascading many basic integrated devices together for future quantum computing, simulation and communication.Among various imperfections, loss is inevitable which is generated from both the essential absorption of materials and the technical problems in fabrication. The effect of loss in bulk optics has been studied in early years [11,12] . When dealing with integrated circuits, many basic optical components are integrated together, and more complex structures should attract our attention. Generally, there are off-chip insertion loss and on-chip waveguide loss. Usually, people summarize all these linear losses and combine them with the inefficiency of detectors. Since quantum processes can be realized via post-selection, which claims successful when detecting the photons in the desired manner, so linear quantum computation can still be performed with those imperfections, and the only influence is the low success probability.In this paper, we studied the general loss model in the on-chip beam splitter (BS) devices and its effects on the gate fidelities. We found that when there is unbalanced loss or shared common loss channel in the BS, there will be significant errors that will affect the performance of the optical quantum processing.For an ideal linear process supported by a quantum PIC, the relation between the input an...