Recent studies have examined problems related to water and fertilizer consumption, including the excessive application of these resources and their use in forest management. Many forest researchers maintain that the choice of suitable irrigation and fertilization strategies for seedling culture and field planting could save water and improve production. Catalpa bungei is a common, high-quality timber tree. The Chinese government plans to promote large-scale planting of C. bungei in appropriate areas; thus, information about irrigation and fertilization of this species is important. Response surface methodology (RSM) can be used to design experiments, establish models, assess significance, and determine optimal conditions. In addition, RSM can be used to analyze how process variables affect responses and to generate three-dimensional plots. Rotatable central composite design (RCCD) is a common experimental method for studying the relationship between plant growth and soil water or fertilizer. Here, we used RCCD for a pot experiment with three factors, five levels, and 20 runs to examine leaf net photosynthetic rate (Pn) and SPAD values of C. bungei seedlings (clone 004-1). Mathematical models were established to examine the effects of main factors, monofactors, and the combination of soil water (W), nitrogen (N), and phosphorus (P) application on Pn and SPAD. Both W and N had significant positive effects on leaf Pn and SPAD values (the sequence of main factor effects was N > W); P did not affect these variables significantly. Analysis of monofactor effects showed that the values of leaf Pn and SPAD increased initially and then decreased with increasing N or W, indicating that leaf Pn and SPAD would be limited in seedlings subjected to excessive irrigation and fertilizer application. RSM based on RCCD showed that the interaction W × N had a significant positive effect on leaf Pn and SPAD: Pn values increased gradually with increasing W and N, while SPAD first increased and then decreased. The W × P and N × P interactions had no significant effects on leaf Pn or SPAD. In addition, leaf Pn and SPAD were positively correlated (P < 0.0001). Our results showed that N, rather than W or P, was the most important limiting factor in the growth of C. bungei seedlings, and we conclude that leaf Pn and SPAD in C. bungei can be promoted by rational irrigation and fertilization practices. Our findings provide fundamental information for seedling culture and afforestation of C. bungei.