The Dick effect is an important factor limiting the frequency stability of sequentially-operating atomic frequency standards.Here we study the impact of the Dick effect in the integrating sphere cold atom clock (ISCAC).To reduce the impact of the Dick effect,a 5 MHz local oscillator with ultra-low phase noise is selected and a new microwave synthesizer is built in-house.Consequently,the phase noise of microwave signal is optimized.The contribution of the Dick effect is reduced to 2.5 × 10-13T-1/2 (T is the integrating time).The frequency stability of 4.6 × 10-13T-1/2 is achieved.The development of this optimization can promote the space applications of the compact ISCAC.