Objectives Overuse of phosphorus (P) fertilizer is common in vegetable production, causing low use efficiency and high environmental risks. It is great significance to study suitable P fertilization rates that matched with appropriate application methods.

Methods A two-year field experiment was conducted in the typical red soil of southwest China, taking pepper (Capsicum annuum L.) as the test materials. Five P basal fertilization treatments were set up: broadcasting P₂O₅ 300 kg/hm² (B300), broadcasting P₂O₅ 150 kg/hm² (B150), broadcasting P₂O₅ 100 kg/hm² (B100), drill applying P₂O₅ 100 kg/hm² (I100), drill applying N and P together at P₂O₅ rate 100 kg/hm² (L100), a no P application control (CK) was made at the same time. The pepper fruit yield, biomass, P content were measured at harvest stage, and P use efficiency, soil P surplus, P index, economic income were calculated.

Results All the five P treatments were recorded similar pepper fruit yields, regardless P rate and application methods, and B150, I100 and L100 were recorded significantly higher pepper yield than CK. Compared with CK, the I100 and L100 treatment increased fruit biomass significantly, but there was no significant difference in fruit biomass among the five P treatments. I100 treatment achieved the highest economic benefit the two years’ of experiment. P application rate had no effect on the P content of various parts of peppers, but L100 treatment significantly increased P accumulation in the pepper fruit, and thereby achieved the highest agronomic efficiency and partial factor productivity of P fertilizer, while B300 achieved the lowest values. P application rate affected P surplus significantly but P application methods did not in the two years. B300 led to the highest P surplus in soil (116.4 kg/hm²), while the other four P treatments reduced the surplus by 59.5%−82.1%, compared to B300. Based on P index, the P loss risk level of I100, L100 was low, and other P treatments were medium.

Conclusions Reducing P fertilizer input from 300 to 100 kg/hm², and replacing broadcast method with drill application would not impact pepper yield, but improve the P use efficiency greatly due to the reduced P fertilizer input and surplus in soil, and increase the economic benefit of pepper at last.