The invention discloses a structured light illuminating microscopic imaging system based on an integrated photonic chip. The structured light illuminating microscopic imaging system comprises a light source, the integrated photonic chip, a sample containing table, a microobjective, a filter part, a photoelectric detector, a computer processing system and a control system. The light source is connected with the integrated photonic chip, the integrated photonic chip is arranged below the sample containing table, the microobjective is arranged above the sample containing table, the filter part is arranged above the microobjective, and the photoelectric detector is arranged above the filter part. A sample to be detected is fixed to the sample containing table, and light emitted by the light source irradiates the sample to be detected on the sample containing table after being processed by the integrated photonic chip. The computer processing system is connected with the sample containing table, the photoelectric detector and the control system. The integrated photonic chip is connected with the control system. According to the technical scheme, the system has the advantages of being small in size, compact in structure, high in system stability, high in solar energy utilization rate, high in imaging resolution ratio and the like, and is suitable for the real-time three-dimensional imaging study of living cells.