Tomato variety“ Hezuo 906” was used as the test material， rice husk ash， peat and vermiculite were mixed as a cultivation substrate according to 5∶3∶2(volume percentage)， and no application of bio-organic fertilizer was used as control， the effects of different addition ratios(1%，2%，4%，8%) of bio-organic fertilizer on the physical and chemical properties of the substrates， the growth of tomato seedlings，photosynthetic pigment content，chlorophyll fluorescence parameters and enzyme activity in the leaves were studied.The results showed that， compared to control， the application of bio-organic fertilizer significantly improved the root vigor and seedling index of tomato seedlings， the net photosynthetic rate， stomatal conductance and transpiration rate of tomato leaves， and the effect of 4% bio-organic fertilizer addition was the best.The addition of 4% bio-organic fertilizer significantly improved ΦPSII and Fv ′/Fm ′ in tomato seedling leaves， and the activities of carbonic anhydrase and Rubisco were also enhanced.It can be seen that the addition of 4% bio-organic fertilizer can regulate the photosynthetic enzyme activity of tomato leaves， increase the content of photosynthetic pigments， increase the photosynthetic capacity， and promote the growth and development of tomato seedlings.It can be used as the optimal addition amount for tomato plug seedlings.